mirror of
https://github.com/alanorth/cgspace-notes.git
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720 lines
123 KiB
XML
720 lines
123 KiB
XML
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<title>CGSpace Notes</title>
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<link>https://alanorth.github.io/cgspace-notes/</link>
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<description>Recent content on CGSpace Notes</description>
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<generator>Hugo -- gohugo.io</generator>
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<language>en-us</language>
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<item>
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<title>December, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-12/</link>
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<pubDate>Fri, 01 Dec 2023 08:48:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-12/</guid>
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<description>2023-12-01 There is still high load on CGSpace and I don&rsquo;t know why I don&rsquo;t see a high number of sessions compared to previous days in the last few weeks $ for file in dspace.log.2023-11-[23]*; do echo &#34;$file&#34;; grep -a -oE &#39;session_id=[A-Z0-9]{32}&#39; &#34;$file&#34; | sort | uniq | wc -l; done dspace.log.2023-11-20 22865 dspace.log.2023-11-21 20296 dspace.log.2023-11-22 19688 dspace.log.2023-11-23 17906 dspace.log.2023-11-24 18453 dspace.log.2023-11-25 17513 dspace.log.2023-11-26 19037 dspace.log.2023-11-27 21103 dspace.log.2023-11-28 23023 dspace.log.2023-11-29 23545 dspace.</description>
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</item>
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<item>
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<title>November, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-11/</link>
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<pubDate>Thu, 02 Nov 2023 12:59:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-11/</guid>
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<description><h2 id="2023-11-01">2023-11-01</h2>
<ul>
<li>Work a bit on the ETL pipeline for the CGIAR Climate Change Synthesis
<ul>
<li>I improved the filtering and wrote some Python using pandas to merge my sources more reliably</li>
</ul>
</li>
</ul>
<h2 id="2023-11-02">2023-11-02</h2>
<ul>
<li>Export CGSpace to check missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul></description>
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</item>
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<item>
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<title>October, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-10/</link>
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<pubDate>Mon, 02 Oct 2023 09:05:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-10/</guid>
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<description><h2 id="2023-10-02">2023-10-02</h2>
<ul>
<li>Export CGSpace to check DOIs against Crossref
<ul>
<li>I found that <a href="https://www.crossref.org/documentation/retrieve-metadata/rest-api/rest-api-metadata-license-information/">Crossref&rsquo;s metadata is in the public domain under the CC0 license</a></li>
<li>One interesting thing is the abstracts, which are copyrighted by the copyright owner, meaning Crossref cannot waive the copyright under the terms of the CC0 license, because it is not theirs to waive</li>
<li>We can be on the safe side by using only abstracts for items that are licensed under Creative Commons</li>
</ul>
</li>
</ul></description>
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</item>
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<item>
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<title>September, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-09/</link>
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<pubDate>Sat, 02 Sep 2023 17:29:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-09/</guid>
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<description><h2 id="2023-09-02">2023-09-02</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul></description>
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</item>
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<item>
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<title>August, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-08/</link>
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<pubDate>Thu, 03 Aug 2023 11:18:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-08/</guid>
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<description><h2 id="2023-08-03">2023-08-03</h2>
<ul>
<li>I finally got around to working on Peter&rsquo;s cleanups for affiliations, authors, and donors from last week
<ul>
<li>I did some minor cleanups myself and applied them to CGSpace</li>
</ul>
</li>
<li>Start working on some batch uploads for IFPRI</li>
</ul></description>
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</item>
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<item>
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<title>July, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-07/</link>
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<pubDate>Sat, 01 Jul 2023 17:14:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-07/</guid>
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<description>2023-07-01 Export CGSpace to check for missing Initiative collection mappings Start harvesting on AReS 2023-07-02 Minor edits to the crossref_doi_lookup.py script while running some checks from 22,000 CGSpace DOIs 2023-07-03 I analyzed the licenses declared by Crossref and found with high confidence that ~400 of ours were incorrect I took the more accurate ones from Crossref and updated the items on CGSpace I took a few hundred ISBNs as well for where we were missing them I also tagged ~4,700 items with missing licenses as &ldquo;Copyrighted; all rights reserved&rdquo; based on their Crossref license status being TDM, mostly from Elsevier, Wiley, and Springer Checking a dozen or so manually, I confirmed that if Crossref only has a TDM license then it&rsquo;s usually copyrighted (could still be open access, but we can&rsquo;t tell via Crossref) I would be curious to write a script to check the Unpaywall API for open access status&hellip; In the past I found that their license status was not very accurate, but the open access status might be more reliable More minor work on the DSpace 7 item views I learned some new Angular template syntax I created a custom component to show Creative Commons licenses on the simple item page I also decided that I don&rsquo;t like the Impact Area icons as a component because they don&rsquo;t have any visual meaning 2023-07-04 Focus group meeting with CGSpace partners about DSpace 7 I added a themed file selection component to the CGSpace theme It displays the bistream description instead of the file name, just like we did in DSpace 6 XMLUI I added a custom component to show share icons 2023-07-05 I spent some time trying to update OpenRXV from Angular 9 to 10 to 11 to 12 to 13 Most things work but there are some minor bugs it seems Mishell from CIP emailed me to say she was having problems approving an item on CGSpace Looking at PostgreSQL I saw there were a dozen or so locks that were several hours and even over one day old so I killed those processes and told her to try again 2023-07-06 Types meeting I wrote a Python script to check Unpaywall for some information about DOIs 2023-07-7 Continue exploring Unpaywall data for some of our DOIs In the past I&rsquo;ve found their licensing information to not be very reliable (preferring Crossref), but I think their open access status is more reliable, especially when the provider is listed as being the publisher Even so, sometimes the version can be &ldquo;acceptedVersion&rdquo;, which is presumably the author&rsquo;s version, as opposed to the &ldquo;publishedVersion&rdquo;, which means it&rsquo;s available as open access on the publisher&rsquo;s website I did some quality assurance and found ~100 that were marked as Limited Access, but should have been Open Access, and fixed a handful of licenses Delete duplicate metadata as describe in my DSpace issue from last year: https://github.</description>
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</item>
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<item>
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<title>June, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-06/</link>
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<pubDate>Fri, 02 Jun 2023 10:29:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-06/</guid>
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<description><h2 id="2023-06-02">2023-06-02</h2>
<ul>
<li>Spend some time testing my <code>post_bitstreams.py</code> script to update thumbnails for items on CGSpace
<ul>
<li>Interestingly I found an item with a JFIF thumbnail and another with a WebP thumbnail&hellip;</li>
</ul>
</li>
<li>Meeting with Valentina, Stefano, and Sara about MODS metadata in CGSpace
<ul>
<li>They have experience with improving the MODS interface in MELSpace&rsquo;s OAI-PMH for use with AGRIS and were curious if we could do the same in CGSpace</li>
<li>From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then just add a bunch of our fields to the crosswalk</li>
</ul>
</li>
</ul></description>
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</item>
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<item>
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<title>May, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-05/</link>
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<pubDate>Wed, 03 May 2023 08:53:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-05/</guid>
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<description><h2 id="2023-05-03">2023-05-03</h2>
<ul>
<li>Alliance&rsquo;s TIP team emailed me to ask about issues authenticating on CGSpace
<ul>
<li>It seems their password expired, which is annoying</li>
</ul>
</li>
<li>I continued looking at the CGSpace subjects for the FAO / AGROVOC exercise that I started last week
<ul>
<li>There are many of our subjects that would match if they added a &ldquo;-&rdquo; like &ldquo;high yielding varieties&rdquo; or used singular&hellip;</li>
<li>Also I found at least two spelling mistakes, for example &ldquo;decison support systems&rdquo;, which would match if it was spelled correctly</li>
</ul>
</li>
<li>Work on cleaning, proofing, and uploading twenty-seven records for IFPRI to CGSpace</li>
</ul></description>
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</item>
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<item>
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<title>April, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-04/</link>
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<pubDate>Sun, 02 Apr 2023 08:19:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-04/</guid>
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<description><h2 id="2023-04-02">2023-04-02</h2>
<ul>
<li>Run all system updates on CGSpace and reboot it</li>
<li>I exported CGSpace to CSV to check for any missing Initiative collection mappings
<ul>
<li>I also did a check for missing country/region mappings with csv-metadata-quality</li>
</ul>
</li>
<li>Start a harvest on AReS</li>
</ul></description>
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</item>
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<item>
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<title>March, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-03/</link>
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<pubDate>Wed, 01 Mar 2023 07:58:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-03/</guid>
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<description><h2 id="2023-03-01">2023-03-01</h2>
<ul>
<li>Remove <code>cg.subject.wle</code> and <code>cg.identifier.wletheme</code> from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)</li>
<li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28">iso-codes 4.13.0 was released</a>, which incorporates my changes to the common names for Iran, Laos, and Syria</li>
<li>I finally got through with porting the input form from DSpace 6 to DSpace 7</li>
</ul></description>
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</item>
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<item>
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<title>February, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-02/</link>
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<pubDate>Wed, 01 Feb 2023 10:57:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-02/</guid>
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<description><h2 id="2023-02-01">2023-02-01</h2>
<ul>
<li>Export CGSpace to cross check the DOI metadata with Crossref
<ul>
<li>I want to try to expand my use of their data to journals, publishers, volumes, issues, etc&hellip;</li>
</ul>
</li>
</ul></description>
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</item>
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<item>
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<title>January, 2023</title>
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<link>https://alanorth.github.io/cgspace-notes/2023-01/</link>
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<pubDate>Sun, 01 Jan 2023 08:44:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2023-01/</guid>
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<description><h2 id="2023-01-01">2023-01-01</h2>
<ul>
<li>Apply some more ORCID identifiers to items on CGSpace using my <code>2022-09-22-add-orcids.csv</code> file
<ul>
<li>I want to update all ORCID names and refresh them in the database</li>
<li>I see we have some new ones that aren&rsquo;t in our list if I combine with this file:</li>
</ul>
</li>
</ul></description>
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</item>
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<item>
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<title>December, 2022</title>
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<link>https://alanorth.github.io/cgspace-notes/2022-12/</link>
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<pubDate>Thu, 01 Dec 2022 08:52:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2022-12/</guid>
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<description><h2 id="2022-12-01">2022-12-01</h2>
<ul>
<li>Fix some incorrect regions on CGSpace
<ul>
<li>I exported the CCAFS and IITA communities, extracted just the country and region columns, then ran them through csv-metadata-quality to fix the regions</li>
</ul>
</li>
<li>Add a few more authors to my CSV with author names and ORCID identifiers and tag 283 items!</li>
<li>Replace &ldquo;East Asia&rdquo; with &ldquo;Eastern Asia&rdquo; region on CGSpace (UN M.49 region)</li>
</ul></description>
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</item>
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<item>
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<title>November, 2022</title>
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<link>https://alanorth.github.io/cgspace-notes/2022-11/</link>
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<pubDate>Tue, 01 Nov 2022 09:11:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2022-11/</guid>
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<description><h2 id="2022-11-01">2022-11-01</h2>
<ul>
<li>Last night I re-synced DSpace 7 Test from CGSpace
<ul>
<li>I also updated all my local <code>7_x-dev</code> branches on the latest upstreams</li>
</ul>
</li>
<li>I spent some time updating the authorizations in Alliance collections
<ul>
<li>I want to make sure they use groups instead of individuals where possible!</li>
</ul>
</li>
<li>I reverted the Cocoon autosave change because it was more of a nuissance that Peter can&rsquo;t upload CSVs from the web interface and is a very low severity security issue</li>
</ul></description>
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</item>
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<item>
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<title>October, 2022</title>
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<link>https://alanorth.github.io/cgspace-notes/2022-10/</link>
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<pubDate>Sat, 01 Oct 2022 19:45:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2022-10/</guid>
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<description><h2 id="2022-10-01">2022-10-01</h2>
<ul>
<li>Start a harvest on AReS last night</li>
<li>Yesterday I realized how to use <a href="https://im4java.sourceforge.net/docs/dev-guide.html">GraphicsMagick with im4java</a> and I want to re-visit some of my thumbnail tests
<ul>
<li>I&rsquo;m also interested in libvips support via jVips, though last time I checked it was only for Java 8</li>
<li>I filed <a href="https://github.com/criteo/JVips/issues/141">an issue to ask about Java 11+ support</a></li>
</ul>
</li>
</ul></description>
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</item>
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<item>
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<title>September, 2022</title>
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<link>https://alanorth.github.io/cgspace-notes/2022-09/</link>
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<pubDate>Thu, 01 Sep 2022 09:41:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2022-09/</guid>
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<description><h2 id="2022-09-01">2022-09-01</h2>
<ul>
<li>A bit of work on the &ldquo;Mapping CG Core–CGSpace–MEL–MARLO Types&rdquo; spreadsheet</li>
<li>I tested an item submission on DSpace Test with the Cocoon <code>org.apache.cocoon.uploads.autosave=false</code> change
<ul>
<li>The submission works as expected</li>
</ul>
</li>
<li>Start debugging some region-related issues with csv-metadata-quality
<ul>
<li>I created a new test file <code>test-geography.csv</code> with some different scenarios</li>
<li>I also fixed a few bugs and improved the region-matching logic</li>
</ul>
</li>
</ul></description>
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</item>
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<item>
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<title>August, 2022</title>
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<link>https://alanorth.github.io/cgspace-notes/2022-08/</link>
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<pubDate>Mon, 01 Aug 2022 10:22:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2022-08/</guid>
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<description><h2 id="2022-08-01">2022-08-01</h2>
<ul>
<li>Our request to add <a href="https://github.com/spdx/license-list-XML/issues/1525">CC-BY-3.0-IGO to SPDX</a> was approved a few weeks ago</li>
</ul></description>
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</item>
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<item>
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<title>July, 2022</title>
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<link>https://alanorth.github.io/cgspace-notes/2022-07/</link>
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<pubDate>Sat, 02 Jul 2022 14:07:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2022-07/</guid>
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<description><h2 id="2022-07-02">2022-07-02</h2>
<ul>
<li>I learned how to use the Levenshtein functions in PostgreSQL
<ul>
<li>The thing is that there is a limit of 255 characters for these functions in PostgreSQL so you need to truncate the strings before comparing</li>
<li>Also, the trgm functions I&rsquo;ve used before are case insensitive, but Levenshtein is not, so you need to make sure to lower case both strings first</li>
</ul>
</li>
</ul></description>
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</item>
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<item>
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<title>June, 2022</title>
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<link>https://alanorth.github.io/cgspace-notes/2022-06/</link>
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<pubDate>Mon, 06 Jun 2022 09:01:36 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2022-06/</guid>
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<description><h2 id="2022-06-06">2022-06-06</h2>
<ul>
<li>Look at the Solr statistics on CGSpace
<ul>
<li>I see 167,000 hits from a bunch of Microsoft IPs with reverse DNS &ldquo;msnbot-&rdquo; using the Solr query <code>dns:*msnbot* AND dns:*.msn.com</code></li>
<li>I purged these first so I could see the other &ldquo;real&rdquo; IPs in the Solr facets</li>
</ul>
</li>
<li>I see 47,500 hits from 80.248.237.167 on a data center ISP in Sweden, using a normal user agent</li>
<li>I see 13,000 hits from 163.237.216.11 on a data center ISP in Australia, using a normal user agent</li>
<li>I see 7,300 hits from 208.185.238.57 from Britanica, using a normal user agent
<ul>
<li>There seem to be many more of these:</li>
</ul>
</li>
</ul></description>
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</item>
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<item>
|
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<title>May, 2022</title>
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<link>https://alanorth.github.io/cgspace-notes/2022-05/</link>
|
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<pubDate>Wed, 04 May 2022 09:13:39 +0300</pubDate>
|
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<guid>https://alanorth.github.io/cgspace-notes/2022-05/</guid>
|
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<description><h2 id="2022-05-04">2022-05-04</h2>
<ul>
<li>I found a few more IPs making requests using the shady Chrome 44 user agent in the last few days so I will add them to the block list too:
<ul>
<li>18.207.136.176</li>
<li>185.189.36.248</li>
<li>50.118.223.78</li>
<li>52.70.76.123</li>
<li>3.236.10.11</li>
</ul>
</li>
<li>Looking at the Solr statistics for 2022-04
<ul>
<li>52.191.137.59 is Microsoft, but they are using a normal user agent and making tens of thousands of requests</li>
<li>64.39.98.62 is owned by Qualys, and all their requests are probing for /etc/passwd etc</li>
<li>185.192.69.15 is in the Netherlands and is using a normal user agent, but making excessive automated HTTP requests to paths forbidden in robots.txt</li>
<li>157.55.39.159 is owned by Microsoft and identifies as bingbot so I don&rsquo;t know why its requests were logged in Solr</li>
<li>52.233.67.176 is owned by Microsoft and uses a normal user agent, but making excessive automated HTTP requests</li>
<li>157.55.39.144 is owned by Microsoft and uses a normal user agent, but making excessive automated HTTP requests</li>
<li>207.46.13.177 is owned by Microsoft and identifies as bingbot so I don&rsquo;t know why its requests were logged in Solr</li>
<li>If I query Solr for <code>time:2022-04* AND dns:*msnbot* AND dns:*.msn.com.</code> I see a handful of IPs that made 41,000 requests</li>
</ul>
</li>
<li>I purged 93,974 hits from these IPs using my <code>check-spider-ip-hits.sh</code> script</li>
</ul></description>
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</item>
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<item>
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<title>April, 2022</title>
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<link>https://alanorth.github.io/cgspace-notes/2022-04/</link>
|
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<pubDate>Fri, 01 Apr 2022 10:53:39 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2022-04/</guid>
|
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<description>2022-04-01 I did G1GC tests on DSpace Test (linode26) to compliment the CMS tests I did yesterday The Discovery indexing took this long: real 334m33.625s user 227m51.331s sys 3m43.037s 2022-04-04 Start a full harvest on AReS Help Marianne with submit/approve access on a new collection on CGSpace Go back in Gaia&rsquo;s batch reports to find records that she indicated for replacing on CGSpace (ie, those with better new copies, new versions, etc) Looking at the Solr statistics for 2022-03 on CGSpace I see 54.</description>
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</item>
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<item>
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<title>March, 2022</title>
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<link>https://alanorth.github.io/cgspace-notes/2022-03/</link>
|
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<pubDate>Tue, 01 Mar 2022 16:46:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2022-03/</guid>
|
||
<description><h2 id="2022-03-01">2022-03-01</h2>
<ul>
<li>Send Gaia the last batch of potential duplicates for items 701 to 980:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ csvcut -c id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv &gt; /tmp/tac4.csv
</span></span><span style="display:flex;"><span>$ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p <span style="color:#e6db74">&#39;fuuu&#39;</span> -o /tmp/2022-03-01-tac-batch4-701-980.csv
</span></span><span style="display:flex;"><span>$ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv &gt; /tmp/tac4-filenames.csv
</span></span><span style="display:flex;"><span>$ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv &gt; /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
</span></span></code></pre></div></description>
|
||
</item>
|
||
<item>
|
||
<title>February, 2022</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2022-02/</link>
|
||
<pubDate>Tue, 01 Feb 2022 14:06:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2022-02/</guid>
|
||
<description><h2 id="2022-02-01">2022-02-01</h2>
<ul>
<li>Meeting with Peter and Abenet about CGSpace in the One CGIAR
<ul>
<li>We agreed to buy $5,000 worth of credits from Atmire for future upgrades</li>
<li>We agreed to move CRPs and non-CGIAR communities off the home page, as well as some other things for the CGIAR System Organization</li>
<li>We agreed to make a Discovery facet for CGIAR Action Areas above the existing CGIAR Impact Areas one</li>
<li>We agreed to try to do more alignment of affiliations/funders with ROR</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>January, 2022</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2022-01/</link>
|
||
<pubDate>Sat, 01 Jan 2022 15:20:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2022-01/</guid>
|
||
<description><h2 id="2022-01-01">2022-01-01</h2>
<ul>
<li>Start a full harvest on AReS</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>December, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-12/</link>
|
||
<pubDate>Wed, 01 Dec 2021 16:07:07 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-12/</guid>
|
||
<description><h2 id="2021-12-01">2021-12-01</h2>
<ul>
<li>Atmire merged some changes I had submitted to the COUNTER-Robots project</li>
<li>I updated our local spider user agents and then re-ran the list with my <code>check-spider-hits.sh</code> script on CGSpace:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ ./ilri/check-spider-hits.sh -f /tmp/agents -p 
</span></span><span style="display:flex;"><span>Purging 1989 hits from The Knowledge AI in statistics
</span></span><span style="display:flex;"><span>Purging 1235 hits from MaCoCu in statistics
</span></span><span style="display:flex;"><span>Purging 455 hits from WhatsApp in statistics
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 3679
</span></span></code></pre></div></description>
|
||
</item>
|
||
<item>
|
||
<title>November, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-11/</link>
|
||
<pubDate>Tue, 02 Nov 2021 22:27:07 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-11/</guid>
|
||
<description><h2 id="2021-11-02">2021-11-02</h2>
<ul>
<li>I experimented with manually sharding the Solr statistics on DSpace Test</li>
<li>First I exported all the 2019 stats from CGSpace:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ ./run.sh -s http://localhost:8081/solr/statistics -f <span style="color:#e6db74">&#39;time:2019-*&#39;</span> -a export -o statistics-2019.json -k uid
</span></span><span style="display:flex;"><span>$ zstd statistics-2019.json
</span></span></code></pre></div></description>
|
||
</item>
|
||
<item>
|
||
<title>October, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-10/</link>
|
||
<pubDate>Fri, 01 Oct 2021 11:14:07 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-10/</guid>
|
||
<description><h2 id="2021-10-01">2021-10-01</h2>
<ul>
<li>Export all affiliations on CGSpace and run them against the latest RoR data dump:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>localhost/dspace63= &gt; \COPY (SELECT DISTINCT text_value as &#34;cg.contributor.affiliation&#34;, count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-10-01-affiliations.csv WITH CSV HEADER;
</span></span><span style="display:flex;"><span>$ csvcut -c <span style="color:#ae81ff">1</span> /tmp/2021-10-01-affiliations.csv | sed 1d &gt; /tmp/2021-10-01-affiliations.txt
</span></span><span style="display:flex;"><span>$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
</span></span><span style="display:flex;"><span>ations-matching.csv
</span></span><span style="display:flex;"><span>$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l 
</span></span><span style="display:flex;"><span>1879
</span></span><span style="display:flex;"><span>$ wc -l /tmp/2021-10-01-affiliations.txt 
</span></span><span style="display:flex;"><span>7100 /tmp/2021-10-01-affiliations.txt
</span></span></code></pre></div><ul>
<li>So we have 1879/7100 (26.46%) matching already</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>September, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-09/</link>
|
||
<pubDate>Wed, 01 Sep 2021 09:14:07 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-09/</guid>
|
||
<description><h2 id="2021-09-02">2021-09-02</h2>
<ul>
<li>Troubleshooting the missing Altmetric scores on AReS
<ul>
<li>Turns out that I didn&rsquo;t actually fix them last month because the check for <code>content.altmetric</code> still exists, and I can&rsquo;t access the DOIs using <code>_h.source.DOI</code> for some reason</li>
<li>I can access all other kinds of item metadata using the Elasticsearch label, but not DOI!!!</li>
<li>I will change <code>DOI</code> to <code>tomato</code> in the repository setup and start a re-harvest&hellip; I need to see if this is some kind of reserved word or something&hellip;</li>
<li>Even as <code>tomato</code> I can&rsquo;t access that field as <code>_h.source.tomato</code> in Angular, but it does work as a filter source&hellip; sigh</li>
</ul>
</li>
<li>I&rsquo;m having problems using the OpenRXV API
<ul>
<li>The syntax Moayad showed me last month doesn&rsquo;t seem to honor the search query properly&hellip;</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>August, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-08/</link>
|
||
<pubDate>Sun, 01 Aug 2021 09:01:07 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-08/</guid>
|
||
<description><h2 id="2021-08-01">2021-08-01</h2>
<ul>
<li>Update Docker images on AReS server (linode20) and reboot the server:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span># docker images | grep -v ^REPO | sed <span style="color:#e6db74">&#39;s/ \+/:/g&#39;</span> | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull
</span></span></code></pre></div><ul>
<li>I decided to upgrade linode20 from Ubuntu 18.04 to 20.04</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>July, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-07/</link>
|
||
<pubDate>Thu, 01 Jul 2021 08:53:07 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-07/</guid>
|
||
<description><h2 id="2021-07-01">2021-07-01</h2>
<ul>
<li>Export another list of ALL subjects on CGSpace, including AGROVOC and non-AGROVOC for Enrico:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>localhost/dspace63= &gt; \COPY (SELECT DISTINCT LOWER(text_value) AS subject, count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (119, 120, 127, 122, 128, 125, 135, 203, 208, 210, 215, 123, 236, 242, 187) GROUP BY subject ORDER BY count DESC) to /tmp/2021-07-01-all-subjects.csv WITH CSV HEADER;
</span></span><span style="display:flex;"><span>COPY 20994
</span></span></code></pre></div></description>
|
||
</item>
|
||
<item>
|
||
<title>June, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-06/</link>
|
||
<pubDate>Tue, 01 Jun 2021 10:51:07 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-06/</guid>
|
||
<description><h2 id="2021-06-01">2021-06-01</h2>
<ul>
<li>IWMI notified me that AReS was down with an HTTP 502 error
<ul>
<li>Looking at UptimeRobot I see it has been down for 33 hours, but I never got a notification</li>
<li>I don&rsquo;t see anything in the Elasticsearch container logs, or the systemd journal on the host, but I notice that the <code>angular_nginx</code> container isn&rsquo;t running</li>
<li>I simply started it and AReS was running again:</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>May, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-05/</link>
|
||
<pubDate>Sun, 02 May 2021 09:50:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-05/</guid>
|
||
<description><h2 id="2021-05-01">2021-05-01</h2>
<ul>
<li>I looked at the top user agents and IPs in the Solr statistics for last month and I see these user agents:
<ul>
<li>&ldquo;RI/1.0&rdquo;, 1337</li>
<li>&ldquo;Microsoft Office Word 2014&rdquo;, 941</li>
</ul>
</li>
<li>I will add the RI/1.0 pattern to our DSpace agents overload and purge them from Solr (we had previously seen this agent with 9,000 hits or so in 2020-09), but I think I will leave the Microsoft Word one&hellip; as that&rsquo;s an actual user&hellip;</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>April, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-04/</link>
|
||
<pubDate>Thu, 01 Apr 2021 09:50:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-04/</guid>
|
||
<description><h2 id="2021-04-01">2021-04-01</h2>
<ul>
<li>I wrote a script to query Sherpa&rsquo;s API for our ISSNs: <code>sherpa-issn-lookup.py</code>
<ul>
<li>I&rsquo;m curious to see how the results compare with the results from Crossref yesterday</li>
</ul>
</li>
<li>AReS Explorer was down since this morning, I didn&rsquo;t see anything in the systemd journal
<ul>
<li>I simply took everything down with docker-compose and then back up, and then it was OK</li>
<li>Perhaps one of the containers crashed, I should have looked closer but I was in a hurry</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>March, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-03/</link>
|
||
<pubDate>Mon, 01 Mar 2021 10:13:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-03/</guid>
|
||
<description><h2 id="2021-03-01">2021-03-01</h2>
<ul>
<li>Discuss some OpenRXV issues with Abdullah from CodeObia
<ul>
<li>He&rsquo;s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API</li>
<li>Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>CGSpace CG Core v2 Migration</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/</link>
|
||
<pubDate>Sun, 21 Feb 2021 13:27:35 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/</guid>
|
||
<description><p>Changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2. Implemented on 2021-02-21.</p>
<p>With reference to <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2 draft standard</a> by Marie-Angélique as well as <a href="http://www.dublincore.org/specifications/dublin-core/dcmi-terms/">DCMI DCTERMS</a>.</p></description>
|
||
</item>
|
||
<item>
|
||
<title>February, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-02/</link>
|
||
<pubDate>Mon, 01 Feb 2021 10:13:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-02/</guid>
|
||
<description><h2 id="2021-02-01">2021-02-01</h2>
<ul>
<li>Abenet said that CIP found more duplicate records in their export from AReS
<ul>
<li>I re-opened <a href="https://github.com/ilri/OpenRXV/issues/67">the issue</a> on OpenRXV where we had previously noticed this</li>
<li>The shared link where the duplicates are is here: <a href="https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6">https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6</a></li>
</ul>
</li>
<li>I had a call with CodeObia to discuss the work on OpenRXV</li>
<li>Check the results of the AReS harvesting from last night:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ curl -s <span style="color:#e6db74">&#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#39;</span>
</span></span><span style="display:flex;"><span>{
</span></span><span style="display:flex;"><span> &#34;count&#34; : 100875,
</span></span><span style="display:flex;"><span> &#34;_shards&#34; : {
</span></span><span style="display:flex;"><span> &#34;total&#34; : 1,
</span></span><span style="display:flex;"><span> &#34;successful&#34; : 1,
</span></span><span style="display:flex;"><span> &#34;skipped&#34; : 0,
</span></span><span style="display:flex;"><span> &#34;failed&#34; : 0
</span></span><span style="display:flex;"><span> }
</span></span><span style="display:flex;"><span>}
</span></span></code></pre></div></description>
|
||
</item>
|
||
<item>
|
||
<title>January, 2021</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2021-01/</link>
|
||
<pubDate>Sun, 03 Jan 2021 10:13:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2021-01/</guid>
|
||
<description><h2 id="2021-01-03">2021-01-03</h2>
<ul>
<li>Peter notified me that some filters on AReS were broken again
<ul>
<li>It&rsquo;s the same issue with the field names getting <code>.keyword</code> appended to the end that I already <a href="https://github.com/ilri/OpenRXV/issues/66">filed an issue on OpenRXV about last month</a></li>
<li>I fixed the broken filters (careful to not edit any others, lest they break too!)</li>
</ul>
</li>
<li>Fix an issue with start page number for the DSpace REST API and statistics API in OpenRXV
<ul>
<li>The start page had been &ldquo;1&rdquo; in the UI, but in the backend they were doing some gymnastics to adjust to the zero-based offset/limit/page of the DSpace REST API and the statistics API</li>
<li>I adjusted it to default to 0 and added a note to the admin screen</li>
<li>I realized that this issue was actually causing the first page of 100 statistics to be missing&hellip;</li>
<li>For example, <a href="https://cgspace.cgiar.org/handle/10568/66839">this item</a> has 51 views on CGSpace, but 0 on AReS</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>December, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-12/</link>
|
||
<pubDate>Tue, 01 Dec 2020 11:32:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-12/</guid>
|
||
<description><h2 id="2020-12-01">2020-12-01</h2>
<ul>
<li>Atmire responded about the issue with duplicate data in our Solr statistics
<ul>
<li>They noticed that some records in the statistics-2015 core haven&rsquo;t been migrated with the AtomicStatisticsUpdateCLI tool yet and assumed that I haven&rsquo;t migrated any of the records yet</li>
<li>That&rsquo;s strange, as I checked all ten cores and 2015 is the only one with some unmigrated documents, as according to the <code>cua_version</code> field</li>
<li>I started processing those (about 411,000 records):</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>CGSpace DSpace 6 Upgrade</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/</link>
|
||
<pubDate>Sun, 15 Nov 2020 13:27:35 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/</guid>
|
||
<description><p>Notes about the DSpace 6 upgrade on CGSpace in 2020-11.</p></description>
|
||
</item>
|
||
<item>
|
||
<title>November, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-11/</link>
|
||
<pubDate>Sun, 01 Nov 2020 13:11:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-11/</guid>
|
||
<description><h2 id="2020-11-01">2020-11-01</h2>
<ul>
<li>Continue with processing the statistics-2019 Solr core with the AtomicStatisticsUpdateCLI tool on DSpace Test
<ul>
<li>So far we&rsquo;ve spent at least fifty hours to process the statistics and statistics-2019 core&hellip; wow.</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>October, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-10/</link>
|
||
<pubDate>Tue, 06 Oct 2020 16:55:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-10/</guid>
|
||
<description><h2 id="2020-10-06">2020-10-06</h2>
<ul>
<li>Add tests for the new <code>/items</code> POST handlers to the DSpace 6.x branch of my <a href="https://github.com/ilri/dspace-statistics-api/tree/v6_x">dspace-statistics-api</a>
<ul>
<li>It took a bit of extra work because I had to learn how to mock the responses for when Solr is not available</li>
<li>Tag and release version 1.3.0 on GitHub: <a href="https://github.com/ilri/dspace-statistics-api/releases/tag/v1.3.0">https://github.com/ilri/dspace-statistics-api/releases/tag/v1.3.0</a></li>
</ul>
</li>
<li>Trying to test the changes Atmire sent last week but I had to re-create my local database from a recent CGSpace dump
<ul>
<li>During the FlywayDB migration I got an error:</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>September, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-09/</link>
|
||
<pubDate>Wed, 02 Sep 2020 15:35:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-09/</guid>
|
||
<description><h2 id="2020-09-02">2020-09-02</h2>
<ul>
<li>Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS</li>
<li>The AReS Explorer hasn&rsquo;t updated its index since 2020-08-22 when I last forced it
<ul>
<li>I restarted it again now and told Moayad that the automatic indexing isn&rsquo;t working</li>
</ul>
</li>
<li>Add <code>Alliance of Bioversity International and CIAT</code> to affiliations on CGSpace</li>
<li>Abenet told me that the general search text on AReS doesn&rsquo;t get reset when you use the &ldquo;Reset Filters&rdquo; button
<ul>
<li>I filed a bug on OpenRXV: <a href="https://github.com/ilri/OpenRXV/issues/39">https://github.com/ilri/OpenRXV/issues/39</a></li>
</ul>
</li>
<li>I filed an issue on OpenRXV to make some minor edits to the admin UI: <a href="https://github.com/ilri/OpenRXV/issues/40">https://github.com/ilri/OpenRXV/issues/40</a></li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>August, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-08/</link>
|
||
<pubDate>Sun, 02 Aug 2020 15:35:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-08/</guid>
|
||
<description><h2 id="2020-08-02">2020-08-02</h2>
<ul>
<li>I spent a few days working on a Java-based curation task to tag items with ISO 3166-1 Alpha2 country codes based on their <code>cg.coverage.country</code> text values
<ul>
<li>It looks up the names in ISO 3166-1 first, and then in our CGSpace countries mapping (which has five or so of Peter&rsquo;s preferred &ldquo;display&rdquo; country names)</li>
<li>It implements a &ldquo;force&rdquo; mode too that will clear existing country codes and re-tag everything</li>
<li>It is class based so I can easily add support for other vocabularies, and the technique could even be used for organizations with mappings to ROR and Clarisa&hellip;</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>July, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-07/</link>
|
||
<pubDate>Wed, 01 Jul 2020 10:53:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-07/</guid>
|
||
<description><h2 id="2020-07-01">2020-07-01</h2>
<ul>
<li>A few users noticed that CGSpace wasn&rsquo;t loading items today, item pages seem blank
<ul>
<li>I looked at the PostgreSQL locks but they don&rsquo;t seem unusual</li>
<li>I guess this is the same &ldquo;blank item page&rdquo; issue that we had a few times in 2019 that we never solved</li>
<li>I restarted Tomcat and PostgreSQL and the issue was gone</li>
</ul>
</li>
<li>Since I was restarting Tomcat anyways I decided to redeploy the latest changes from the <code>5_x-prod</code> branch and I added a note about COVID-19 items to the CGSpace frontpage at Peter&rsquo;s request</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>June, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-06/</link>
|
||
<pubDate>Mon, 01 Jun 2020 13:55:39 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-06/</guid>
|
||
<description><h2 id="2020-06-01">2020-06-01</h2>
<ul>
<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
<ul>
<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
</ul>
</li>
<li>In other news, I checked the statistics API on DSpace 6 and it&rsquo;s working</li>
<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>May, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-05/</link>
|
||
<pubDate>Sat, 02 May 2020 09:52:04 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-05/</guid>
|
||
<description><h2 id="2020-05-02">2020-05-02</h2>
<ul>
<li>Peter said that CTA is having problems submitting an item to CGSpace
<ul>
<li>Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in &lsquo;idle in transaction&rsquo; and &lsquo;waiting for lock&rsquo; state are increasing again</li>
<li>I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>April, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-04/</link>
|
||
<pubDate>Thu, 02 Apr 2020 10:53:24 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-04/</guid>
|
||
<description><h2 id="2020-04-02">2020-04-02</h2>
<ul>
<li>Maria asked me to update Charles Staver&rsquo;s ORCID iD in the submission template and on CGSpace, as his name was lower case before, and now he has corrected it
<ul>
<li>I updated the fifty-eight existing items on CGSpace</li>
</ul>
</li>
<li>Looking into the items Udana had asked about last week that were missing Altmetric donuts:
<ul>
<li><a href="https://hdl.handle.net/10568/103225">The first</a> is still missing its DOI, so I added it and <a href="https://twitter.com/mralanorth/status/1245632619661766657">tweeted its handle</a> (after a few hours there was a donut with score 222)</li>
<li><a href="https://hdl.handle.net/10568/106899">The second item</a> now has a donut with score 2 since I <a href="https://twitter.com/mralanorth/status/1243158045540134913">tweeted its handle</a> last week</li>
<li><a href="https://hdl.handle.net/10568/107258">The third item</a> now has a donut with score 1 since I <a href="https://twitter.com/mralanorth/status/1243158786392625153">tweeted it</a> last week</li>
</ul>
</li>
<li>On the same note, the <a href="https://hdl.handle.net/10568/106573">one item</a> Abenet pointed out last week now has a donut with score of 104 after I <a href="https://twitter.com/mralanorth/status/1243163710241345536">tweeted it</a> last week</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>March, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-03/</link>
|
||
<pubDate>Mon, 02 Mar 2020 12:31:30 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-03/</guid>
|
||
<description><h2 id="2020-03-02">2020-03-02</h2>
<ul>
<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
<ul>
<li>Tag version 1.2.0 on GitHub</li>
</ul>
</li>
<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
<ul>
<li>You need to download this into the DSpace 6.x source and compile it</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>February, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-02/</link>
|
||
<pubDate>Sun, 02 Feb 2020 11:56:30 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-02/</guid>
|
||
<description><h2 id="2020-02-02">2020-02-02</h2>
<ul>
<li>Continue working on porting CGSpace&rsquo;s DSpace 5 code to DSpace 6.3 that I started yesterday
<ul>
<li>Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database</li>
<li>I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks</li>
<li>Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff</li>
<li>The code finally builds and runs with a fresh install</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>January, 2020</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2020-01/</link>
|
||
<pubDate>Mon, 06 Jan 2020 10:48:30 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2020-01/</guid>
|
||
<description><h2 id="2020-01-06">2020-01-06</h2>
<ul>
<li>Open <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=706">a ticket</a> with Atmire to request a quote for the upgrade to DSpace 6</li>
<li>Last week Altmetric responded about the <a href="https://hdl.handle.net/10568/97087">item</a> that had a lower score than than its DOI
<ul>
<li>The score is now linked to the DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/81236">item</a> that had the same problem in 2019 has also been fixed</li>
</ul>
</li>
</ul>
<h2 id="2020-01-07">2020-01-07</h2>
<ul>
<li>Peter Ballantyne highlighted one more WLE <a href="https://hdl.handle.net/10568/101286">item</a> that is missing the Altmetric score that its DOI has
<ul>
<li>The DOI has a score of 259, but the Handle has no score at all</li>
<li>I <a href="https://twitter.com/mralanorth/status/1214471427157626881">tweeted</a> the CGSpace repository link</li>
</ul>
</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>December, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-12/</link>
|
||
<pubDate>Sun, 01 Dec 2019 11:22:30 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-12/</guid>
|
||
<description><h2 id="2019-12-01">2019-12-01</h2>
<ul>
<li>Upgrade CGSpace (linode18) to Ubuntu 18.04:
<ul>
<li>Check any packages that have residual configs and purge them:</li>
<li><!-- raw HTML omitted --># dpkg -l | grep -E &lsquo;^rc&rsquo; | awk &lsquo;{print $2}&rsquo; | xargs dpkg -P<!-- raw HTML omitted --></li>
<li>Make sure all packages are up to date and the package manager is up to date, then reboot:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code># apt update &amp;&amp; apt full-upgrade
# apt-get autoremove &amp;&amp; apt-get autoclean
# dpkg -C
# reboot
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>November, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-11/</link>
|
||
<pubDate>Mon, 04 Nov 2019 12:20:30 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-11/</guid>
|
||
<description><h2 id="2019-11-04">2019-11-04</h2>
<ul>
<li>Peter noticed that there were 5.2 million hits on CGSpace in 2019-10 according to the Atmire usage statistics
<ul>
<li>I looked in the nginx logs and see 4.6 million in the access logs, and 1.2 million in the API logs:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code># zcat --force /var/log/nginx/*access.log.*.gz | grep -cE &#34;[0-9]{1,2}/Oct/2019&#34;
4671942
# zcat --force /var/log/nginx/{rest,oai,statistics}.log.*.gz | grep -cE &#34;[0-9]{1,2}/Oct/2019&#34;
1277694
</code></pre><ul>
<li>So 4.6 million from XMLUI and another 1.2 million from API requests</li>
<li>Let&rsquo;s see how many of the REST API requests were for bitstreams (because they are counted in Solr stats):</li>
</ul>
<pre tabindex="0"><code># zcat --force /var/log/nginx/rest.log.*.gz | grep -c -E &#34;[0-9]{1,2}/Oct/2019&#34;
1183456 
# zcat --force /var/log/nginx/rest.log.*.gz | grep -E &#34;[0-9]{1,2}/Oct/2019&#34; | grep -c -E &#34;/rest/bitstreams&#34;
106781
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>October, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-10/</link>
|
||
<pubDate>Tue, 01 Oct 2019 13:20:51 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-10/</guid>
|
||
<description>2019-10-01 Udana from IWMI asked me for a CSV export of their community on CGSpace I exported it, but a quick run through the csv-metadata-quality tool shows that there are some low-hanging fruits we can fix before I send him the data I will limit the scope to the titles, regions, subregions, and river basins for now to manually fix some non-breaking spaces (U+00A0) there that would otherwise be removed by the csv-metadata-quality script&rsquo;s &ldquo;unneccesary Unicode&rdquo; fix: $ csvcut -c &#39;id,dc.</description>
|
||
</item>
|
||
<item>
|
||
<title>September, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-09/</link>
|
||
<pubDate>Sun, 01 Sep 2019 10:17:51 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-09/</guid>
|
||
<description><h2 id="2019-09-01">2019-09-01</h2>
<ul>
<li>Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning</li>
<li>Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:</li>
</ul>
<pre tabindex="0"><code># zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E &#34;01/Sep/2019:0&#34; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
 440 17.58.101.255
 441 157.55.39.101
 485 207.46.13.43
 728 169.60.128.125
 730 207.46.13.108
 758 157.55.39.9
 808 66.160.140.179
 814 207.46.13.212
 2472 163.172.71.23
 6092 3.94.211.189
# zcat --force /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E &#34;01/Sep/2019:0&#34; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
 33 2a01:7e00::f03c:91ff:fe16:fcb
 57 3.83.192.124
 57 3.87.77.25
 57 54.82.1.8
 822 2a01:9cc0:47:1:1a:4:0:2
 1223 45.5.184.72
 1633 172.104.229.92
 5112 205.186.128.185
 7249 2a01:7e00::f03c:91ff:fe18:7396
 9124 45.5.186.2
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>August, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-08/</link>
|
||
<pubDate>Sat, 03 Aug 2019 12:39:51 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-08/</guid>
|
||
<description><h2 id="2019-08-03">2019-08-03</h2>
<ul>
<li>Look at Bioversity&rsquo;s latest migration CSV and now I see that Francesco has cleaned up the extra columns and the newline at the end of the file, but many of the column headers have an extra space in the name&hellip;</li>
</ul>
<h2 id="2019-08-04">2019-08-04</h2>
<ul>
<li>Deploy ORCID identifier updates requested by Bioversity to CGSpace</li>
<li>Run system updates on CGSpace (linode18) and reboot it
<ul>
<li>Before updating it I checked Solr and verified that all statistics cores were loaded properly&hellip;</li>
<li>After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s lucky.</li>
</ul>
</li>
<li>Run system updates on DSpace Test (linode19) and reboot it</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>July, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-07/</link>
|
||
<pubDate>Mon, 01 Jul 2019 12:13:51 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-07/</guid>
|
||
<description><h2 id="2019-07-01">2019-07-01</h2>
<ul>
<li>Create an &ldquo;AfricaRice books and book chapters&rdquo; collection on CGSpace for AfricaRice</li>
<li>Last month Sisay asked why the following &ldquo;most popular&rdquo; statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
<ul>
<li><a href="https://dspacetest.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&amp;time_filter_end_date=01%2F12%2F2018">DSpace Test</a></li>
<li><a href="https://cgspace.cgiar.org/handle/10568/35697/most-popular/item#simplefilter=custom&amp;time_filter_end_date=01%2F12%2F2018">CGSpace</a></li>
</ul>
</li>
<li>Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>June, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-06/</link>
|
||
<pubDate>Sun, 02 Jun 2019 10:57:51 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-06/</guid>
|
||
<description><h2 id="2019-06-02">2019-06-02</h2>
<ul>
<li>Merge the <a href="https://github.com/ilri/DSpace/pull/425">Solr filterCache</a> and <a href="https://github.com/ilri/DSpace/pull/426">XMLUI ISI journal</a> changes to the <code>5_x-prod</code> branch and deploy on CGSpace</li>
<li>Run system updates on CGSpace (linode18) and reboot it</li>
</ul>
<h2 id="2019-06-03">2019-06-03</h2>
<ul>
<li>Skype with Marie-Angélique and Abenet about <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2</a></li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>May, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-05/</link>
|
||
<pubDate>Wed, 01 May 2019 07:37:43 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-05/</guid>
|
||
<description><h2 id="2019-05-01">2019-05-01</h2>
<ul>
<li>Help CCAFS with regenerating some item thumbnails after they uploaded new PDFs to some items on CGSpace</li>
<li>A user on the dspace-tech mailing list offered some suggestions for troubleshooting the problem with the inability to delete certain items
<ul>
<li>Apparently if the item is in the <code>workflowitem</code> table it is submitted to a workflow</li>
<li>And if it is in the <code>workspaceitem</code> table it is in the pre-submitted state</li>
</ul>
</li>
<li>The item seems to be in a pre-submitted state, so I tried to delete it from there:</li>
</ul>
<pre tabindex="0"><code>dspace=# DELETE FROM workspaceitem WHERE item_id=74648;
DELETE 1
</code></pre><ul>
<li>But after this I tried to delete the item from the XMLUI and it is <em>still</em> present&hellip;</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>April, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-04/</link>
|
||
<pubDate>Mon, 01 Apr 2019 09:00:43 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-04/</guid>
|
||
<description><h2 id="2019-04-01">2019-04-01</h2>
<ul>
<li>Meeting with AgroKnow to discuss CGSpace, ILRI data, AReS, GARDIAN, etc
<ul>
<li>They asked if we had plans to enable RDF support in CGSpace</li>
</ul>
</li>
<li>There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today
<ul>
<li>I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep &#39;Spore-192-EN-web.pdf&#39; | grep -E &#39;(18.196.196.108|18.195.78.144|18.195.218.6)&#39; | awk &#39;{print $9}&#39; | sort | uniq -c | sort -n | tail -n 5
 4432 200
</code></pre><ul>
<li>In the last two weeks there have been 47,000 downloads of this <em>same exact PDF</em> by these three IP addresses</li>
<li>Apply country and region corrections and deletions on DSpace Test and CGSpace:</li>
</ul>
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-9-countries.csv -db dspace -u dspace -p &#39;fuuu&#39; -f cg.coverage.country -m 228 -t ACTION -d
$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u dspace -p &#39;fuuu&#39; -f cg.coverage.region -m 231 -t action -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 228 -f cg.coverage.country -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 231 -f cg.coverage.region -d
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>March, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-03/</link>
|
||
<pubDate>Fri, 01 Mar 2019 12:16:30 +0100</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-03/</guid>
|
||
<description><h2 id="2019-03-01">2019-03-01</h2>
<ul>
<li>I checked IITA&rsquo;s 259 Feb 14 records from last month for duplicates using Atmire&rsquo;s Duplicate Checker on a fresh snapshot of CGSpace on my local machine and everything looks good</li>
<li>I am now only waiting to hear from her about where the items should go, though I assume Journal Articles go to IITA Journal Articles collection, etc&hellip;</li>
<li>Looking at the other half of Udana&rsquo;s WLE records from 2018-11
<ul>
<li>I finished the ones for Restoring Degraded Landscapes (RDL), but these are for Variability, Risks and Competing Uses (VRC)</li>
<li>I did the usual cleanups for whitespace, added regions where they made sense for certain countries, cleaned up the DOI link formats, added rights information based on the publications page for a few items</li>
<li>Most worryingly, there are encoding errors in the abstracts for eleven items, for example:</li>
<li>68.15% <20> 9.45 instead of 68.15% ± 9.45</li>
<li>2003<EFBFBD>2013 instead of 2003–2013</li>
</ul>
</li>
<li>I think I will need to ask Udana to re-copy and paste the abstracts with more care using Google Docs</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>February, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-02/</link>
|
||
<pubDate>Fri, 01 Feb 2019 21:37:30 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-02/</guid>
|
||
<description><h2 id="2019-02-01">2019-02-01</h2>
<ul>
<li>Linode has alerted a few times since last night that the CPU usage on CGSpace (linode18) was high despite me increasing the alert threshold last week from 250% to 275%—I might need to increase it again!</li>
<li>The top IPs before, during, and after this latest alert tonight were:</li>
</ul>
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &#34;01/Feb/2019:(17|18|19|20|21)&#34; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
 245 207.46.13.5
 332 54.70.40.11
 385 5.143.231.38
 405 207.46.13.173
 405 207.46.13.75
 1117 66.249.66.219
 1121 35.237.175.180
 1546 5.9.6.51
 2474 45.5.186.2
 5490 85.25.237.71
</code></pre><ul>
<li><code>85.25.237.71</code> is the &ldquo;Linguee Bot&rdquo; that I first saw last month</li>
<li>The Solr statistics the past few months have been very high and I was wondering if the web server logs also showed an increase</li>
<li>There were just over 3 million accesses in the nginx logs last month:</li>
</ul>
<pre tabindex="0"><code># time zcat --force /var/log/nginx/* | grep -cE &#34;[0-9]{1,2}/Jan/2019&#34;
3018243

real 0m19.873s
user 0m22.203s
sys 0m1.979s
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>January, 2019</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2019-01/</link>
|
||
<pubDate>Wed, 02 Jan 2019 09:48:30 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2019-01/</guid>
|
||
<description><h2 id="2019-01-02">2019-01-02</h2>
<ul>
<li>Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning</li>
<li>I don&rsquo;t see anything interesting in the web server logs around that time though:</li>
</ul>
<pre tabindex="0"><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &#34;02/Jan/2019:0(1|2|3)&#34; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
 92 40.77.167.4
 99 210.7.29.100
 120 38.126.157.45
 177 35.237.175.180
 177 40.77.167.32
 216 66.249.75.219
 225 18.203.76.93
 261 46.101.86.248
 357 207.46.13.1
 903 54.70.40.11
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>December, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-12/</link>
|
||
<pubDate>Sun, 02 Dec 2018 02:09:30 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-12/</guid>
|
||
<description><h2 id="2018-12-01">2018-12-01</h2>
<ul>
<li>Switch CGSpace (linode18) to use OpenJDK instead of Oracle JDK</li>
<li>I manually installed OpenJDK, then removed Oracle JDK, then re-ran the <a href="http://github.com/ilri/rmg-ansible-public">Ansible playbook</a> to update all configuration files, etc</li>
<li>Then I ran all system updates and restarted the server</li>
</ul>
<h2 id="2018-12-02">2018-12-02</h2>
<ul>
<li>I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another <a href="https://usn.ubuntu.com/3831-1/">Ghostscript vulnerability last week</a></li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>November, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-11/</link>
|
||
<pubDate>Thu, 01 Nov 2018 16:41:30 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-11/</guid>
|
||
<description><h2 id="2018-11-01">2018-11-01</h2>
<ul>
<li>Finalize AReS Phase I and Phase II ToRs</li>
<li>Send a note about my <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to the dspace-tech mailing list</li>
</ul>
<h2 id="2018-11-03">2018-11-03</h2>
<ul>
<li>Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage</li>
<li>Today these are the top 10 IPs:</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>October, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-10/</link>
|
||
<pubDate>Mon, 01 Oct 2018 22:31:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-10/</guid>
|
||
<description><h2 id="2018-10-01">2018-10-01</h2>
<ul>
<li>Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items</li>
<li>I created a GitHub issue to track this <a href="https://github.com/ilri/DSpace/issues/389">#389</a>, because I&rsquo;m super busy in Nairobi right now</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>September, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-09/</link>
|
||
<pubDate>Sun, 02 Sep 2018 09:55:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-09/</guid>
|
||
<description><h2 id="2018-09-02">2018-09-02</h2>
<ul>
<li>New <a href="https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.5">PostgreSQL JDBC driver version 42.2.5</a></li>
<li>I&rsquo;ll update the DSpace role in our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> and run the updated playbooks on CGSpace and DSpace Test</li>
<li>Also, I&rsquo;ll re-run the <code>postgresql</code> tasks because the custom PostgreSQL variables are dynamic according to the system&rsquo;s RAM, and we never re-ran them after migrating to larger Linodes last month</li>
<li>I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I&rsquo;m getting those autowire errors in Tomcat 8.5.30 again:</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>August, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-08/</link>
|
||
<pubDate>Wed, 01 Aug 2018 11:52:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-08/</guid>
|
||
<description><h2 id="2018-08-01">2018-08-01</h2>
<ul>
<li>DSpace Test had crashed at some point yesterday morning and I see the following in <code>dmesg</code>:</li>
</ul>
<pre tabindex="0"><code>[Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
</code></pre><ul>
<li>Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight</li>
<li>From the DSpace log I see that eventually Solr stopped responding, so I guess the <code>java</code> process that was OOM killed above was Tomcat&rsquo;s</li>
<li>I&rsquo;m not sure why Tomcat didn&rsquo;t crash with an OutOfMemoryError&hellip;</li>
<li>Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core</li>
<li>The server only has 8GB of RAM so we&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;ll start starving the OS, PostgreSQL, and command line batch processes</li>
<li>I ran all system updates on DSpace Test and rebooted it</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>July, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-07/</link>
|
||
<pubDate>Sun, 01 Jul 2018 12:56:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-07/</guid>
|
||
<description><h2 id="2018-07-01">2018-07-01</h2>
<ul>
<li>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</li>
</ul>
<pre tabindex="0"><code>$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
</code></pre><ul>
<li>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</li>
</ul>
<pre tabindex="0"><code>There is insufficient memory for the Java Runtime Environment to continue.
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>June, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-06/</link>
|
||
<pubDate>Mon, 04 Jun 2018 19:49:54 -0700</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-06/</guid>
|
||
<description><h2 id="2018-06-04">2018-06-04</h2>
<ul>
<li>Test the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">DSpace 5.8 module upgrades from Atmire</a> (<a href="https://github.com/ilri/DSpace/pull/378">#378</a>)
<ul>
<li>There seems to be a problem with the CUA and L&amp;R versions in <code>pom.xml</code> because they are using SNAPSHOT and it doesn&rsquo;t build</li>
</ul>
</li>
<li>I added the new CCAFS Phase II Project Tag <code>PII-FP1_PACCA2</code> and merged it into the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/379">#379</a>)</li>
<li>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</li>
</ul>
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p &#39;fuuu&#39; -f dc.contributor.author -t correct -m 3 -n
</code></pre><ul>
<li>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="https://alanorth.github.io/cgspace-notes/cgspace-notes/2018-03/">March, 2018</a></li>
<li>Time to index ~70,000 items on CGSpace:</li>
</ul>
<pre tabindex="0"><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b 

real 74m42.646s
user 8m5.056s
sys 2m7.289s
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>May, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-05/</link>
|
||
<pubDate>Tue, 01 May 2018 16:43:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-05/</guid>
|
||
<description><h2 id="2018-05-01">2018-05-01</h2>
<ul>
<li>I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
<ul>
<li>http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E</li>
<li>http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E</li>
</ul>
</li>
<li>Then I reduced the JVM heap size from 6144 back to 5120m</li>
<li>Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> to support hosts choosing which distribution they want to use</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>April, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-04/</link>
|
||
<pubDate>Sun, 01 Apr 2018 16:13:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-04/</guid>
|
||
<description><h2 id="2018-04-01">2018-04-01</h2>
<ul>
<li>I tried to test something on DSpace Test but noticed that it&rsquo;s down since god knows when</li>
<li>Catalina logs at least show some memory errors yesterday:</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>March, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-03/</link>
|
||
<pubDate>Fri, 02 Mar 2018 16:07:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-03/</guid>
|
||
<description><h2 id="2018-03-02">2018-03-02</h2>
<ul>
<li>Export a CSV of the IITA community metadata for Martin Mueller</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>February, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-02/</link>
|
||
<pubDate>Thu, 01 Feb 2018 16:28:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-02/</guid>
|
||
<description><h2 id="2018-02-01">2018-02-01</h2>
<ul>
<li>Peter gave feedback on the <code>dc.rights</code> proof of concept that I had sent him last week</li>
<li>We don&rsquo;t need to distinguish between internal and external works, so that makes it just a simple list</li>
<li>Yesterday I figured out how to monitor DSpace sessions using JMX</li>
<li>I copied the logic in the <code>jmx_tomcat_dbpools</code> provided by Ubuntu&rsquo;s <code>munin-plugins-java</code> package and used the stuff I discovered about JMX <a href="https://alanorth.github.io/cgspace-notes/cgspace-notes/2018-01/">in 2018-01</a></li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>January, 2018</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2018-01/</link>
|
||
<pubDate>Tue, 02 Jan 2018 08:35:54 -0800</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2018-01/</guid>
|
||
<description><h2 id="2018-01-02">2018-01-02</h2>
<ul>
<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
<li>I didn&rsquo;t get any load alerts from Linode and the REST and XMLUI logs don&rsquo;t show anything out of the ordinary</li>
<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
<li>In dspace.log around that time I see many errors like &ldquo;Client closed the connection before file download was complete&rdquo;</li>
<li>And just before that I see this:</li>
</ul>
<pre tabindex="0"><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
</code></pre><ul>
<li>Ah hah! So the pool was actually empty!</li>
<li>I need to increase that, let&rsquo;s try to bump it up from 50 to 75</li>
<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don&rsquo;t know what the hell Uptime Robot saw</li>
<li>I notice this error quite a few times in dspace.log:</li>
</ul>
<pre tabindex="0"><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse &#39;dateIssued_keyword:[1976+TO+1979]&#39;: Encountered &#34; &#34;]&#34; &#34;] &#34;&#34; at line 1, column 32.
</code></pre><ul>
<li>And there are many of these errors every day for the past month:</li>
</ul>
<pre tabindex="0"><code>$ grep -c &#34;Error while searching for sidebar facets&#34; dspace.log.*
dspace.log.2017-11-21:4
dspace.log.2017-11-22:1
dspace.log.2017-11-23:4
dspace.log.2017-11-24:11
dspace.log.2017-11-25:0
dspace.log.2017-11-26:1
dspace.log.2017-11-27:7
dspace.log.2017-11-28:21
dspace.log.2017-11-29:31
dspace.log.2017-11-30:15
dspace.log.2017-12-01:15
dspace.log.2017-12-02:20
dspace.log.2017-12-03:38
dspace.log.2017-12-04:65
dspace.log.2017-12-05:43
dspace.log.2017-12-06:72
dspace.log.2017-12-07:27
dspace.log.2017-12-08:15
dspace.log.2017-12-09:29
dspace.log.2017-12-10:35
dspace.log.2017-12-11:20
dspace.log.2017-12-12:44
dspace.log.2017-12-13:36
dspace.log.2017-12-14:59
dspace.log.2017-12-15:104
dspace.log.2017-12-16:53
dspace.log.2017-12-17:66
dspace.log.2017-12-18:83
dspace.log.2017-12-19:101
dspace.log.2017-12-20:74
dspace.log.2017-12-21:55
dspace.log.2017-12-22:66
dspace.log.2017-12-23:50
dspace.log.2017-12-24:85
dspace.log.2017-12-25:62
dspace.log.2017-12-26:49
dspace.log.2017-12-27:30
dspace.log.2017-12-28:54
dspace.log.2017-12-29:68
dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34
</code></pre><ul>
<li>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let&rsquo;s Encrypt if it&rsquo;s just a handful of domains</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>December, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-12/</link>
|
||
<pubDate>Fri, 01 Dec 2017 13:53:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-12/</guid>
|
||
<description><h2 id="2017-12-01">2017-12-01</h2>
<ul>
<li>Uptime Robot noticed that CGSpace went down</li>
<li>The logs say &ldquo;Timeout waiting for idle object&rdquo;</li>
<li>PostgreSQL activity says there are 115 connections currently</li>
<li>The list of connections to XMLUI and REST API for today:</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>November, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-11/</link>
|
||
<pubDate>Thu, 02 Nov 2017 09:37:54 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-11/</guid>
|
||
<description><h2 id="2017-11-01">2017-11-01</h2>
<ul>
<li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li>
</ul>
<h2 id="2017-11-02">2017-11-02</h2>
<ul>
<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
</ul>
<pre tabindex="0"><code># grep -c &#34;CORE&#34; /var/log/nginx/access.log
0
</code></pre><ul>
<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
</ul>
<pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>October, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-10/</link>
|
||
<pubDate>Sun, 01 Oct 2017 08:07:54 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-10/</guid>
|
||
<description><h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
</ul>
<pre tabindex="0"><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre><ul>
<li>There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</li>
<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>CGIAR Library Migration</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/cgiar-library-migration/</link>
|
||
<pubDate>Mon, 18 Sep 2017 16:38:35 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/cgiar-library-migration/</guid>
|
||
<description><p>Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called <em>CGIAR System Organization</em>.</p></description>
|
||
</item>
|
||
<item>
|
||
<title>September, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-09/</link>
|
||
<pubDate>Thu, 07 Sep 2017 16:54:52 +0700</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-09/</guid>
|
||
<description><h2 id="2017-09-06">2017-09-06</h2>
<ul>
<li>Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two hours</li>
</ul>
<h2 id="2017-09-07">2017-09-07</h2>
<ul>
<li>Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account is both in the approvers step as well as the group</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>August, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-08/</link>
|
||
<pubDate>Tue, 01 Aug 2017 11:51:52 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-08/</guid>
|
||
<description><h2 id="2017-08-01">2017-08-01</h2>
<ul>
<li>Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours</li>
<li>I looked in the Activity pane of the Admin Control Panel and it seems that Google, Baidu, Yahoo, and Bing are all crawling with massive numbers of bots concurrently (~100 total, mostly Baidu and Google)</li>
<li>The good thing is that, according to <code>dspace.log.2017-08-01</code>, they are all using the same Tomcat session</li>
<li>This means our Tomcat Crawler Session Valve is working</li>
<li>But many of the bots are browsing dynamic URLs like:
<ul>
<li>/handle/10568/3353/discover</li>
<li>/handle/10568/16510/browse</li>
</ul>
</li>
<li>The <code>robots.txt</code> only blocks the top-level <code>/discover</code> and <code>/browse</code> URLs&hellip; we will need to find a way to forbid them from accessing these!</li>
<li>Relevant issue from DSpace Jira (semi resolved in DSpace 6.0): <a href="https://jira.duraspace.org/browse/DS-2962">https://jira.duraspace.org/browse/DS-2962</a></li>
<li>It turns out that we&rsquo;re already adding the <code>X-Robots-Tag &quot;none&quot;</code> HTTP header, but this only forbids the search engine from <em>indexing</em> the page, not crawling it!</li>
<li>Also, the bot has to successfully browse the page first so it can receive the HTTP header&hellip;</li>
<li>We might actually have to <em>block</em> these requests with HTTP 403 depending on the user agent</li>
<li>Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415</li>
<li>This was due to newline characters in the <code>dc.description.abstract</code> column, which caused OpenRefine to choke when exporting the CSV</li>
<li>I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using <code>g/^$/d</code></li>
<li>Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>July, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-07/</link>
|
||
<pubDate>Sat, 01 Jul 2017 18:03:52 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-07/</guid>
|
||
<description><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&rsquo;s MEL DSpace database so we can compare fields with CGSpace</li>
<li>We can use PostgreSQL&rsquo;s extended output format (<code>-x</code>) plus <code>sed</code> to format the output into quasi XML:</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>June, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-06/</link>
|
||
<pubDate>Thu, 01 Jun 2017 10:14:52 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-06/</guid>
|
||
<description>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&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; 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.</description>
|
||
</item>
|
||
<item>
|
||
<title>May, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-05/</link>
|
||
<pubDate>Mon, 01 May 2017 16:21:52 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-05/</guid>
|
||
<description>2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace.</description>
|
||
</item>
|
||
<item>
|
||
<title>April, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-04/</link>
|
||
<pubDate>Sun, 02 Apr 2017 17:08:52 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-04/</guid>
|
||
<description><h2 id="2017-04-02">2017-04-02</h2>
<ul>
<li>Merge one change to CCAFS flagships that I had forgotten to remove last month (&ldquo;MANAGING CLIMATE RISK&rdquo;): <a href="https://github.com/ilri/DSpace/pull/317">https://github.com/ilri/DSpace/pull/317</a></li>
<li>Quick proof-of-concept hack to add <code>dc.rights</code> to the input form, including some inline instructions/hints:</li>
</ul>
<p><img src="https://alanorth.github.io/cgspace-notes/cgspace-notes/2017/04/dc-rights.png" alt="dc.rights in the submission form"></p>
<ul>
<li>Remove redundant/duplicate text in the DSpace submission license</li>
<li>Testing the CMYK patch on a collection with 650 items:</li>
</ul>
<pre tabindex="0"><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &#34;ImageMagick PDF Thumbnail&#34; -v &gt;&amp; /tmp/filter-media-cmyk.txt
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>March, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-03/</link>
|
||
<pubDate>Wed, 01 Mar 2017 17:08:52 +0200</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-03/</guid>
|
||
<description><h2 id="2017-03-01">2017-03-01</h2>
<ul>
<li>Run the 279 CIAT author corrections on CGSpace</li>
</ul>
<h2 id="2017-03-02">2017-03-02</h2>
<ul>
<li>Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace</li>
<li>CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles</li>
<li>They might come in at the top level in one &ldquo;CGIAR System&rdquo; community, or with several communities</li>
<li>I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?</li>
<li>Need to send Peter and Michael some notes about this in a few days</li>
<li>Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI</li>
<li>Filed an issue on DSpace issue tracker for the <code>filter-media</code> bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: <a href="https://jira.duraspace.org/browse/DS-3516">DS-3516</a></li>
<li>Discovered that the ImageMagic <code>filter-media</code> plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK</li>
<li>Interestingly, it seems DSpace 4.x&rsquo;s thumbnails were sRGB, but forcing regeneration using DSpace 5.x&rsquo;s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see <a href="https://cgspace.cgiar.org/handle/10568/51999">10568/51999</a>):</li>
</ul>
<pre tabindex="0"><code>$ identify ~/Desktop/alc_contrastes_desafios.jpg
/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>February, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-02/</link>
|
||
<pubDate>Tue, 07 Feb 2017 07:04:52 -0800</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-02/</guid>
|
||
<description><h2 id="2017-02-07">2017-02-07</h2>
<ul>
<li>An item was mapped twice erroneously again, so I had to remove one of the mappings manually:</li>
</ul>
<pre tabindex="0"><code>dspace=# select * from collection2item where item_id = &#39;80278&#39;;
 id | collection_id | item_id
-------+---------------+---------
 92551 | 313 | 80278
 92550 | 313 | 80278
 90774 | 1051 | 80278
(3 rows)
dspace=# delete from collection2item where id = 92551 and item_id = 80278;
DELETE 1
</code></pre><ul>
<li>Create issue on GitHub to track the addition of CCAFS Phase II project tags (<a href="https://github.com/ilri/DSpace/issues/301">#301</a>)</li>
<li>Looks like we&rsquo;ll be using <code>cg.identifier.ccafsprojectpii</code> as the field name</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>January, 2017</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2017-01/</link>
|
||
<pubDate>Mon, 02 Jan 2017 10:43:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2017-01/</guid>
|
||
<description><h2 id="2017-01-02">2017-01-02</h2>
<ul>
<li>I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error</li>
<li>I tested on DSpace Test as well and it doesn&rsquo;t work there either</li>
<li>I asked on the dspace-tech mailing list because it seems to be broken, and actually now I&rsquo;m not sure if we&rsquo;ve ever had the sharding task run successfully over all these years</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>December, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-12/</link>
|
||
<pubDate>Fri, 02 Dec 2016 10:43:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-12/</guid>
|
||
<description><h2 id="2016-12-02">2016-12-02</h2>
<ul>
<li>CGSpace was down for five hours in the morning while I was sleeping</li>
<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
</ul>
<pre tabindex="0"><code>2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&#34;TX157907838689377964651674089851855413607&#34;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail=&#34;dc.title&#34;, transactionID=&#34;TX157907838689377964651674089851855413607&#34;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail=&#34;THUMBNAIL&#34;, transactionID=&#34;TX157907838689377964651674089851855413607&#34;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail=&#34;-1&#34;, transactionID=&#34;TX157907838689377964651674089851855413607&#34;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID=&#34;TX157907838689377964651674089851855413607&#34;)
</code></pre><ul>
<li>I see thousands of them in the logs for the last few months, so it&rsquo;s not related to the DSpace 5.5 upgrade</li>
<li>I&rsquo;ve raised a ticket with Atmire to ask</li>
<li>Another worrying error from dspace.log is:</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>November, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-11/</link>
|
||
<pubDate>Tue, 01 Nov 2016 09:21:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-11/</guid>
|
||
<description><h2 id="2016-11-01">2016-11-01</h2>
<ul>
<li>Add <code>dc.type</code> to the output options for Atmire&rsquo;s Listings and Reports module (<a href="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
</ul>
<p><img src="https://alanorth.github.io/cgspace-notes/cgspace-notes/2016/11/listings-and-reports.png" alt="Listings and Reports with output type"></p></description>
|
||
</item>
|
||
<item>
|
||
<title>October, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-10/</link>
|
||
<pubDate>Mon, 03 Oct 2016 15:53:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-10/</guid>
|
||
<description><h2 id="2016-10-03">2016-10-03</h2>
<ul>
<li>Testing adding <a href="https://wiki.lyrasis.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing">ORCIDs to a CSV</a> file for a single item to see if the author orders get messed up</li>
<li>Need to test the following scenarios to see how author order is affected:
<ul>
<li>ORCIDs only</li>
<li>ORCIDs plus normal authors</li>
</ul>
</li>
<li>I exported a random item&rsquo;s metadata as CSV, deleted <em>all columns</em> except id and collection, and made a new coloum called <code>ORCID:dc.contributor.author</code> with the following random ORCIDs from the ORCID registry:</li>
</ul>
<pre tabindex="0"><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>September, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-09/</link>
|
||
<pubDate>Thu, 01 Sep 2016 15:53:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-09/</guid>
|
||
<description><h2 id="2016-09-01">2016-09-01</h2>
<ul>
<li>Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors</li>
<li>Discuss how the migration of CGIAR&rsquo;s Active Directory to a flat structure will break our LDAP groups in DSpace</li>
<li>We had been using <code>DC=ILRI</code> to determine whether a user was ILRI or not</li>
<li>It looks like we might be able to use OUs now, instead of DCs:</li>
</ul>
<pre tabindex="0"><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &#34;dc=cgiarad,dc=org&#34; -D &#34;admigration1@cgiarad.org&#34; -W &#34;(sAMAccountName=admigration1)&#34;
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>August, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-08/</link>
|
||
<pubDate>Mon, 01 Aug 2016 15:53:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-08/</guid>
|
||
<description><h2 id="2016-08-01">2016-08-01</h2>
<ul>
<li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li>
<li>Play with upgrading Mirage 2 dependencies in <code>bower.json</code> because most are several versions of out date</li>
<li>Bootstrap is at 3.3.0 but upstream is at 3.3.7, and upgrading to anything beyond 3.3.1 breaks glyphicons and probably more</li>
<li>bower stuff is a dead end, waste of time, too many issues</li>
<li>Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of <code>fonts</code>)</li>
<li>Start working on DSpace 5.1 → 5.5 port:</li>
</ul>
<pre tabindex="0"><code>$ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>July, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-07/</link>
|
||
<pubDate>Fri, 01 Jul 2016 10:53:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-07/</guid>
|
||
<description><h2 id="2016-07-01">2016-07-01</h2>
<ul>
<li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li>
<li>I think this query should find and replace all authors that have &ldquo;,&rdquo; at the end of their names:</li>
</ul>
<pre tabindex="0"><code>dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, &#39;(^.+?),$&#39;, &#39;\1&#39;) where metadata_field_id=3 and resource_type_id=2 and text_value ~ &#39;^.+?,$&#39;;
UPDATE 95
dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value ~ &#39;^.+?,$&#39;;
 text_value
------------
(0 rows)
</code></pre><ul>
<li>In this case the select query was showing 95 results before the update</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>June, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-06/</link>
|
||
<pubDate>Wed, 01 Jun 2016 10:53:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-06/</guid>
|
||
<description><h2 id="2016-06-01">2016-06-01</h2>
<ul>
<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
<li>After reading the <a href="https://www.oclc.org/support/services/contentdm/help/server-admin-help/oai-support.en.html">ContentDM documentation</a> I found IFPRI&rsquo;s OAI endpoint: <a href="http://ebrary.ifpri.org/oai/oai.php">http://ebrary.ifpri.org/oai/oai.php</a></li>
<li>After reading the <a href="https://www.openarchives.org/OAI/openarchivesprotocol.html">OAI documentation</a> and testing with an <a href="http://validator.oaipmh.com/">OAI validator</a> I found out how to get their publications</li>
<li>This is their publications set: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc">http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc</a></li>
<li>You can see the others by using the OAI <code>ListSets</code> verb: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListSets">http://ebrary.ifpri.org/oai/oai.php?verb=ListSets</a></li>
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>May, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-05/</link>
|
||
<pubDate>Sun, 01 May 2016 23:06:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-05/</guid>
|
||
<description><h2 id="2016-05-01">2016-05-01</h2>
<ul>
<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
<li>I have blocked access to the API now</li>
<li>There are 3,000 IPs accessing the REST API in a 24-hour period!</li>
</ul>
<pre tabindex="0"><code># awk &#39;{print $1}&#39; /var/log/nginx/rest.log | uniq | wc -l
3168
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>April, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-04/</link>
|
||
<pubDate>Mon, 04 Apr 2016 11:06:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-04/</guid>
|
||
<description><h2 id="2016-04-04">2016-04-04</h2>
<ul>
<li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li>
<li>We are backing up all logs in the log folder, including useless stuff like solr, cocoon, handle-plugin, etc</li>
<li>After running DSpace for over five years I&rsquo;ve never needed to look in any other log file than dspace.log, leave alone one from last year!</li>
<li>This will save us a few gigs of backup space we&rsquo;re paying for on S3</li>
<li>Also, I noticed the <code>checker</code> log has some errors we should pay attention to:</li>
</ul></description>
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</item>
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<item>
|
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<title>March, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-03/</link>
|
||
<pubDate>Wed, 02 Mar 2016 16:50:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-03/</guid>
|
||
<description><h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
<li>For some reason we still have the <code>index-lucene-update</code> cron job active on CGSpace, but I&rsquo;m pretty sure we don&rsquo;t need it as of the latest few versions of Atmire&rsquo;s Listings and Reports module</li>
<li>Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>February, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-02/</link>
|
||
<pubDate>Fri, 05 Feb 2016 13:18:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-02/</guid>
|
||
<description><h2 id="2016-02-05">2016-02-05</h2>
<ul>
<li>Looking at some DAGRIS data for Abenet Yabowork</li>
<li>Lots of issues with spaces, newlines, etc causing the import to fail</li>
<li>I noticed we have a very <em>interesting</em> list of countries on CGSpace:</li>
</ul>
<p><img src="https://alanorth.github.io/cgspace-notes/cgspace-notes/2016/02/cgspace-countries.png" alt="CGSpace country list"></p>
<ul>
<li>Not only are there 49,000 countries, we have some blanks (25)&hellip;</li>
<li>Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>January, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-01/</link>
|
||
<pubDate>Wed, 13 Jan 2016 13:18:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-01/</guid>
|
||
<description><h2 id="2016-01-13">2016-01-13</h2>
<ul>
<li>Move ILRI collection <code>10568/12503</code> from <code>10568/27869</code> to <code>10568/27629</code> using the <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">move_collections.sh</a> script I wrote last year.</li>
<li>I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated.</li>
<li>Update GitHub wiki for documentation of <a href="https://github.com/ilri/DSpace/wiki/Maintenance-Tasks">maintenance tasks</a>.</li>
</ul></description>
|
||
</item>
|
||
<item>
|
||
<title>December, 2015</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2015-12/</link>
|
||
<pubDate>Wed, 02 Dec 2015 13:18:00 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2015-12/</guid>
|
||
<description><h2 id="2015-12-02">2015-12-02</h2>
<ul>
<li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li>
</ul>
<pre tabindex="0"><code># cd /home/dspacetest.cgiar.org/log
# ls -lh dspace.log.2015-11-18*
-rw-rw-r-- 1 tomcat7 tomcat7 2.0M Nov 18 23:59 dspace.log.2015-11-18
-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
</code></pre></description>
|
||
</item>
|
||
<item>
|
||
<title>November, 2015</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2015-11/</link>
|
||
<pubDate>Mon, 23 Nov 2015 17:00:57 +0300</pubDate>
|
||
<guid>https://alanorth.github.io/cgspace-notes/2015-11/</guid>
|
||
<description><h2 id="2015-11-22">2015-11-22</h2>
<ul>
<li>CGSpace went down</li>
<li>Looks like DSpace exhausted its PostgreSQL connection pool</li>
<li>Last week I had increased the limit from 30 to 60, which seemed to help, but now there are many more idle connections:</li>
</ul>
<pre tabindex="0"><code>$ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspace
78
</code></pre></description>
|
||
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