# Notes on CGSpace Notes

https://alanorth.github.io/cgspace-notes/categories/notes/ Recent content in Notes on CGSpace Notes Hugo -- gohugo.io en-us Tue, 19 Mar 2024 16:24:20 +0300

# March, 2024

https://alanorth.github.io/cgspace-notes/2024-03/ Fri, 01 Mar 2024 09:55:00 +0300 https://alanorth.github.io/cgspace-notes/2024-03/ <h2 id="2024-03-01">2024-03-01</h2> <ul> <li>Last week Bizu reported an issue with the &ldquo;browse by issue date&rdquo; drop down <ul> <li>I verified it, and suspect it could be due to missing issue dates&hellip;</li> <li>It might be this issue: <a href="https://github.com/DSpace/dspace-angular/issues/2808">https://github.com/DSpace/dspace-angular/issues/2808</a></li> </ul> </li> </ul>

# February, 2024

https://alanorth.github.io/cgspace-notes/2024-02/ Mon, 05 Feb 2024 11:10:00 +0300 https://alanorth.github.io/cgspace-notes/2024-02/ <h2 id="2024-02-05">2024-02-05</h2> <ul> <li>Delete duplicate metadata as described in my DSpace issue from last year: <a href="https://github.com/DSpace/DSpace/issues/8253">https://github.com/DSpace/DSpace/issues/8253</a></li> <li>Lower case all the AGROVOC subjects on CGSpace</li> </ul>

# January, 2024

https://alanorth.github.io/cgspace-notes/2024-01/ Tue, 02 Jan 2024 10:08:00 +0300 https://alanorth.github.io/cgspace-notes/2024-01/ <h2 id="2024-01-02">2024-01-02</h2> <ul> <li>Work on preparation of new server for DSpace 7 migration <ul> <li>I&rsquo;m not quite sure what we need to do for the Handle server</li> <li>For now I just ran the <code>dspace make-handle-config</code> script and diffed it with the one from DSpace 6</li> <li>I sent the bundle to the Handle admins to make sure it&rsquo;s OK before we do the migration</li> </ul> </li> <li>Continue testing and debugging the cgspace-java-helpers on DSpace 7</li> <li>Work on IFPRI ISNAR archive cleanup</li> </ul>

# December, 2023

https://alanorth.github.io/cgspace-notes/2023-12/ Fri, 01 Dec 2023 08:48:36 +0300 https://alanorth.github.io/cgspace-notes/2023-12/ 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.

# November, 2023

https://alanorth.github.io/cgspace-notes/2023-11/ Thu, 02 Nov 2023 12:59:36 +0300 https://alanorth.github.io/cgspace-notes/2023-11/ <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>

# October, 2023

https://alanorth.github.io/cgspace-notes/2023-10/ Mon, 02 Oct 2023 09:05:36 +0300 https://alanorth.github.io/cgspace-notes/2023-10/ <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>

# September, 2023

https://alanorth.github.io/cgspace-notes/2023-09/ Sat, 02 Sep 2023 17:29:36 +0300 https://alanorth.github.io/cgspace-notes/2023-09/ <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>

# August, 2023

https://alanorth.github.io/cgspace-notes/2023-08/ Thu, 03 Aug 2023 11:18:36 +0300 https://alanorth.github.io/cgspace-notes/2023-08/ <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>

# July, 2023

https://alanorth.github.io/cgspace-notes/2023-07/ Sat, 01 Jul 2023 17:14:36 +0300 https://alanorth.github.io/cgspace-notes/2023-07/ 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 described in my DSpace issue from last year: https://github.

# June, 2023

https://alanorth.github.io/cgspace-notes/2023-06/ Fri, 02 Jun 2023 10:29:36 +0300 https://alanorth.github.io/cgspace-notes/2023-06/ <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>

# May, 2023

https://alanorth.github.io/cgspace-notes/2023-05/ Wed, 03 May 2023 08:53:36 +0300 https://alanorth.github.io/cgspace-notes/2023-05/ <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>

# April, 2023

https://alanorth.github.io/cgspace-notes/2023-04/ Sun, 02 Apr 2023 08:19:36 +0300 https://alanorth.github.io/cgspace-notes/2023-04/ <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>

# March, 2023

https://alanorth.github.io/cgspace-notes/2023-03/ Wed, 01 Mar 2023 07:58:36 +0300 https://alanorth.github.io/cgspace-notes/2023-03/ <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>

# February, 2023

https://alanorth.github.io/cgspace-notes/2023-02/ Wed, 01 Feb 2023 10:57:36 +0300 https://alanorth.github.io/cgspace-notes/2023-02/ <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>

# January, 2023

https://alanorth.github.io/cgspace-notes/2023-01/ Sun, 01 Jan 2023 08:44:36 +0300 https://alanorth.github.io/cgspace-notes/2023-01/ <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>

# December, 2022

https://alanorth.github.io/cgspace-notes/2022-12/ Thu, 01 Dec 2022 08:52:36 +0300 https://alanorth.github.io/cgspace-notes/2022-12/ <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>

# November, 2022

https://alanorth.github.io/cgspace-notes/2022-11/ Tue, 01 Nov 2022 09:11:36 +0300 https://alanorth.github.io/cgspace-notes/2022-11/ <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>

# October, 2022

https://alanorth.github.io/cgspace-notes/2022-10/ Sat, 01 Oct 2022 19:45:36 +0300 https://alanorth.github.io/cgspace-notes/2022-10/ <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>

# September, 2022

https://alanorth.github.io/cgspace-notes/2022-09/ Thu, 01 Sep 2022 09:41:36 +0300 https://alanorth.github.io/cgspace-notes/2022-09/ <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>

# August, 2022

https://alanorth.github.io/cgspace-notes/2022-08/ Mon, 01 Aug 2022 10:22:36 +0300 https://alanorth.github.io/cgspace-notes/2022-08/ <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>

# July, 2022

https://alanorth.github.io/cgspace-notes/2022-07/ Sat, 02 Jul 2022 14:07:36 +0300 https://alanorth.github.io/cgspace-notes/2022-07/ <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>

# June, 2022

https://alanorth.github.io/cgspace-notes/2022-06/ Mon, 06 Jun 2022 09:01:36 +0300 https://alanorth.github.io/cgspace-notes/2022-06/ <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>

# May, 2022

https://alanorth.github.io/cgspace-notes/2022-05/ Wed, 04 May 2022 09:13:39 +0300 https://alanorth.github.io/cgspace-notes/2022-05/ <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>

# April, 2022

https://alanorth.github.io/cgspace-notes/2022-04/ Fri, 01 Apr 2022 10:53:39 +0300 https://alanorth.github.io/cgspace-notes/2022-04/ 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.

# March, 2022

https://alanorth.github.io/cgspace-notes/2022-03/ Tue, 01 Mar 2022 16:46:54 +0300 https://alanorth.github.io/cgspace-notes/2022-03/ <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>

# February, 2022

https://alanorth.github.io/cgspace-notes/2022-02/ Tue, 01 Feb 2022 14:06:54 +0200 https://alanorth.github.io/cgspace-notes/2022-02/ <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>

# January, 2022

https://alanorth.github.io/cgspace-notes/2022-01/ Sat, 01 Jan 2022 15:20:54 +0200 https://alanorth.github.io/cgspace-notes/2022-01/ <h2 id="2022-01-01">2022-01-01</h2> <ul> <li>Start a full harvest on AReS</li> </ul>

# December, 2021

https://alanorth.github.io/cgspace-notes/2021-12/ Wed, 01 Dec 2021 16:07:07 +0200 https://alanorth.github.io/cgspace-notes/2021-12/ <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>

# November, 2021

https://alanorth.github.io/cgspace-notes/2021-11/ Tue, 02 Nov 2021 22:27:07 +0200 https://alanorth.github.io/cgspace-notes/2021-11/ <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>

# October, 2021

https://alanorth.github.io/cgspace-notes/2021-10/ Fri, 01 Oct 2021 11:14:07 +0300 https://alanorth.github.io/cgspace-notes/2021-10/ <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>

# September, 2021

https://alanorth.github.io/cgspace-notes/2021-09/ Wed, 01 Sep 2021 09:14:07 +0300 https://alanorth.github.io/cgspace-notes/2021-09/ <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>

# August, 2021

https://alanorth.github.io/cgspace-notes/2021-08/ Sun, 01 Aug 2021 09:01:07 +0300 https://alanorth.github.io/cgspace-notes/2021-08/ <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>

# July, 2021

https://alanorth.github.io/cgspace-notes/2021-07/ Thu, 01 Jul 2021 08:53:07 +0300 https://alanorth.github.io/cgspace-notes/2021-07/ <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>

# June, 2021

https://alanorth.github.io/cgspace-notes/2021-06/ Tue, 01 Jun 2021 10:51:07 +0300 https://alanorth.github.io/cgspace-notes/2021-06/ <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>

# May, 2021

https://alanorth.github.io/cgspace-notes/2021-05/ Sun, 02 May 2021 09:50:54 +0300 https://alanorth.github.io/cgspace-notes/2021-05/ <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>

# April, 2021

https://alanorth.github.io/cgspace-notes/2021-04/ Thu, 01 Apr 2021 09:50:54 +0300 https://alanorth.github.io/cgspace-notes/2021-04/ <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>

# March, 2021

https://alanorth.github.io/cgspace-notes/2021-03/ Mon, 01 Mar 2021 10:13:54 +0200 https://alanorth.github.io/cgspace-notes/2021-03/ <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>

# CGSpace CG Core v2 Migration

https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/ Sun, 21 Feb 2021 13:27:35 +0200 https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/ <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>

# February, 2021

https://alanorth.github.io/cgspace-notes/2021-02/ Mon, 01 Feb 2021 10:13:54 +0200 https://alanorth.github.io/cgspace-notes/2021-02/ <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>

# January, 2021

https://alanorth.github.io/cgspace-notes/2021-01/ Sun, 03 Jan 2021 10:13:54 +0200 https://alanorth.github.io/cgspace-notes/2021-01/ <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>

# December, 2020

https://alanorth.github.io/cgspace-notes/2020-12/ Tue, 01 Dec 2020 11:32:54 +0200 https://alanorth.github.io/cgspace-notes/2020-12/ <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>

# CGSpace DSpace 6 Upgrade

https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/ Sun, 15 Nov 2020 13:27:35 +0200 https://alanorth.github.io/cgspace-notes/cgspace-dspace6-upgrade/ <p>Notes about the DSpace 6 upgrade on CGSpace in 2020-11.</p>

# November, 2020

https://alanorth.github.io/cgspace-notes/2020-11/ Sun, 01 Nov 2020 13:11:54 +0200 https://alanorth.github.io/cgspace-notes/2020-11/ <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>

# October, 2020

https://alanorth.github.io/cgspace-notes/2020-10/ Tue, 06 Oct 2020 16:55:54 +0300 https://alanorth.github.io/cgspace-notes/2020-10/ <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>

# September, 2020

https://alanorth.github.io/cgspace-notes/2020-09/ Wed, 02 Sep 2020 15:35:54 +0300 https://alanorth.github.io/cgspace-notes/2020-09/ <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>

# August, 2020

https://alanorth.github.io/cgspace-notes/2020-08/ Sun, 02 Aug 2020 15:35:54 +0300 https://alanorth.github.io/cgspace-notes/2020-08/ <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>

# July, 2020

https://alanorth.github.io/cgspace-notes/2020-07/ Wed, 01 Jul 2020 10:53:54 +0300 https://alanorth.github.io/cgspace-notes/2020-07/ <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>

# June, 2020

https://alanorth.github.io/cgspace-notes/2020-06/ Mon, 01 Jun 2020 13:55:39 +0300 https://alanorth.github.io/cgspace-notes/2020-06/ <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>

# May, 2020

https://alanorth.github.io/cgspace-notes/2020-05/ Sat, 02 May 2020 09:52:04 +0300 https://alanorth.github.io/cgspace-notes/2020-05/ <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>

# April, 2020

https://alanorth.github.io/cgspace-notes/2020-04/ Thu, 02 Apr 2020 10:53:24 +0300 https://alanorth.github.io/cgspace-notes/2020-04/ <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>

# March, 2020

https://alanorth.github.io/cgspace-notes/2020-03/ Mon, 02 Mar 2020 12:31:30 +0200 https://alanorth.github.io/cgspace-notes/2020-03/ <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>

# February, 2020

https://alanorth.github.io/cgspace-notes/2020-02/ Sun, 02 Feb 2020 11:56:30 +0200 https://alanorth.github.io/cgspace-notes/2020-02/ <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>

# January, 2020

https://alanorth.github.io/cgspace-notes/2020-01/ Mon, 06 Jan 2020 10:48:30 +0200 https://alanorth.github.io/cgspace-notes/2020-01/ <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>

# December, 2019

https://alanorth.github.io/cgspace-notes/2019-12/ Sun, 01 Dec 2019 11:22:30 +0200 https://alanorth.github.io/cgspace-notes/2019-12/ <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>

# November, 2019

https://alanorth.github.io/cgspace-notes/2019-11/ Mon, 04 Nov 2019 12:20:30 +0200 https://alanorth.github.io/cgspace-notes/2019-11/ <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>

# October, 2019

https://alanorth.github.io/cgspace-notes/2019-10/ Tue, 01 Oct 2019 13:20:51 +0300 https://alanorth.github.io/cgspace-notes/2019-10/ 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.

# September, 2019

https://alanorth.github.io/cgspace-notes/2019-09/ Sun, 01 Sep 2019 10:17:51 +0300 https://alanorth.github.io/cgspace-notes/2019-09/ <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>

# August, 2019

https://alanorth.github.io/cgspace-notes/2019-08/ Sat, 03 Aug 2019 12:39:51 +0300 https://alanorth.github.io/cgspace-notes/2019-08/ <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>

# July, 2019

https://alanorth.github.io/cgspace-notes/2019-07/ Mon, 01 Jul 2019 12:13:51 +0300 https://alanorth.github.io/cgspace-notes/2019-07/ <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>

# June, 2019

https://alanorth.github.io/cgspace-notes/2019-06/ Sun, 02 Jun 2019 10:57:51 +0300 https://alanorth.github.io/cgspace-notes/2019-06/ <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>

# May, 2019

https://alanorth.github.io/cgspace-notes/2019-05/ Wed, 01 May 2019 07:37:43 +0300 https://alanorth.github.io/cgspace-notes/2019-05/ <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>

# April, 2019

https://alanorth.github.io/cgspace-notes/2019-04/ Mon, 01 Apr 2019 09:00:43 +0300 https://alanorth.github.io/cgspace-notes/2019-04/ <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>

# March, 2019

https://alanorth.github.io/cgspace-notes/2019-03/ Fri, 01 Mar 2019 12:16:30 +0100 https://alanorth.github.io/cgspace-notes/2019-03/ <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% � 9.45 instead of 68.15% ± 9.45</li> <li>2003�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>

# February, 2019

https://alanorth.github.io/cgspace-notes/2019-02/ Fri, 01 Feb 2019 21:37:30 +0200 https://alanorth.github.io/cgspace-notes/2019-02/ <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>

# January, 2019

https://alanorth.github.io/cgspace-notes/2019-01/ Wed, 02 Jan 2019 09:48:30 +0200 https://alanorth.github.io/cgspace-notes/2019-01/ <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>

# December, 2018

https://alanorth.github.io/cgspace-notes/2018-12/ Sun, 02 Dec 2018 02:09:30 +0200 https://alanorth.github.io/cgspace-notes/2018-12/ <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>

# November, 2018

https://alanorth.github.io/cgspace-notes/2018-11/ Thu, 01 Nov 2018 16:41:30 +0200 https://alanorth.github.io/cgspace-notes/2018-11/ <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>

# October, 2018

https://alanorth.github.io/cgspace-notes/2018-10/ Mon, 01 Oct 2018 22:31:54 +0300 https://alanorth.github.io/cgspace-notes/2018-10/ <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>

# September, 2018

https://alanorth.github.io/cgspace-notes/2018-09/ Sun, 02 Sep 2018 09:55:54 +0300 https://alanorth.github.io/cgspace-notes/2018-09/ <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>

# August, 2018

https://alanorth.github.io/cgspace-notes/2018-08/ Wed, 01 Aug 2018 11:52:54 +0300 https://alanorth.github.io/cgspace-notes/2018-08/ <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>

# July, 2018

https://alanorth.github.io/cgspace-notes/2018-07/ Sun, 01 Jul 2018 12:56:54 +0300 https://alanorth.github.io/cgspace-notes/2018-07/ <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>

# June, 2018

https://alanorth.github.io/cgspace-notes/2018-06/ Mon, 04 Jun 2018 19:49:54 -0700 https://alanorth.github.io/cgspace-notes/2018-06/ <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>

# May, 2018

https://alanorth.github.io/cgspace-notes/2018-05/ Tue, 01 May 2018 16:43:54 +0300 https://alanorth.github.io/cgspace-notes/2018-05/ <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>

# April, 2018

https://alanorth.github.io/cgspace-notes/2018-04/ Sun, 01 Apr 2018 16:13:54 +0200 https://alanorth.github.io/cgspace-notes/2018-04/ <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>

# March, 2018

https://alanorth.github.io/cgspace-notes/2018-03/ Fri, 02 Mar 2018 16:07:54 +0200 https://alanorth.github.io/cgspace-notes/2018-03/ <h2 id="2018-03-02">2018-03-02</h2> <ul> <li>Export a CSV of the IITA community metadata for Martin Mueller</li> </ul>

# February, 2018

https://alanorth.github.io/cgspace-notes/2018-02/ Thu, 01 Feb 2018 16:28:54 +0200 https://alanorth.github.io/cgspace-notes/2018-02/ <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>

# January, 2018

https://alanorth.github.io/cgspace-notes/2018-01/ Tue, 02 Jan 2018 08:35:54 -0800 https://alanorth.github.io/cgspace-notes/2018-01/ <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>

# December, 2017

https://alanorth.github.io/cgspace-notes/2017-12/ Fri, 01 Dec 2017 13:53:54 +0300 https://alanorth.github.io/cgspace-notes/2017-12/ <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>

# November, 2017

https://alanorth.github.io/cgspace-notes/2017-11/ Thu, 02 Nov 2017 09:37:54 +0200 https://alanorth.github.io/cgspace-notes/2017-11/ <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>

# October, 2017

https://alanorth.github.io/cgspace-notes/2017-10/ Sun, 01 Oct 2017 08:07:54 +0300 https://alanorth.github.io/cgspace-notes/2017-10/ <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>

# CGIAR Library Migration

https://alanorth.github.io/cgspace-notes/cgiar-library-migration/ Mon, 18 Sep 2017 16:38:35 +0300 https://alanorth.github.io/cgspace-notes/cgiar-library-migration/ <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>