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2019-10-11 10:19:42 +02:00
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< h1 class = "blog-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/" rel = "home" > CGSpace Notes< / a > < / h1 >
< p class = "lead blog-description" dir = "auto" > Documenting day-to-day work on the < a href = "https://cgspace.cgiar.org" > CGSpace< / a > repository.< / p >
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2021-10-04 18:40:13 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-10/" > October, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-10-01T11:14:07+03:00" > Fri Oct 01, 2021< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< 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 >
< pre tabindex = "0" > < code class = "language-console" data-lang = "console" > localhost/dspace63= > \COPY (SELECT DISTINCT text_value as " cg.contributor.affiliation" , 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;
$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d > /tmp/2021-10-01-affiliations.txt
$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
ations-matching.csv
$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
1879
$ wc -l /tmp/2021-10-01-affiliations.txt
7100 /tmp/2021-10-01-affiliations.txt
< / code > < / pre > < ul >
< li > So we have 1879/7100 (26.46%) matching already< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-10/' > Read more →< / a >
< / article >
2021-09-02 16:21:48 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-09/" > September, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-09-01T09:14:07+03:00" > Wed Sep 01, 2021< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< 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’ t actually fix them last month because the check for < code > content.altmetric< / code > still exists, and I can’ 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… I need to see if this is some kind of reserved word or something… < / li >
2021-09-04 20:16:03 +02:00
< li > Even as < code > tomato< / code > I can’ t access that field as < code > _h.source.tomato< / code > in Angular, but it does work as a filter source… sigh< / li >
2021-09-02 16:21:48 +02:00
< / ul >
< / li >
< li > I’ m having problems using the OpenRXV API
< ul >
< li > The syntax Moayad showed me last month doesn’ t seem to honor the search query properly… < / li >
< / ul >
< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-09/' > Read more →< / a >
< / article >
2021-08-01 15:19:05 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-08/" > August, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-08-01T09:01:07+03:00" > Sun Aug 01, 2021< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< h2 id = "2021-08-01" > 2021-08-01< / h2 >
< ul >
< li > Update Docker images on AReS server (linode20) and reboot the server:< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code class = "language-console" data-lang = "console" > # docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull
2021-08-01 15:19:05 +02:00
< / code > < / pre > < ul >
< li > I decided to upgrade linode20 from Ubuntu 18.04 to 20.04< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-08/' > Read more →< / a >
< / article >
2021-06-03 20:54:49 +02:00
< article class = "blog-post" >
< header >
2021-07-20 10:05:03 +02:00
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-07/" > July, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-07-01T08:53:07+03:00" > Thu Jul 01, 2021< / time > by Alan Orth in
2021-06-03 20:54:49 +02:00
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
2021-07-20 10:05:03 +02:00
< h2 id = "2021-07-01" > 2021-07-01< / h2 >
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< ul >
2021-07-20 10:05:03 +02:00
< li > Export another list of ALL subjects on CGSpace, including AGROVOC and non-AGROVOC for Enrico:< / li >
2021-06-03 20:54:49 +02:00
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code class = "language-console" data-lang = "console" > localhost/dspace63= > \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;
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COPY 20994
< / code > < / pre >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-07/' > Read more →< / a >
2021-06-03 20:54:49 +02:00
< / article >
2021-07-07 15:30:06 +02:00
< article class = "blog-post" >
< header >
2021-07-20 10:05:03 +02:00
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-06/" > June, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-06-01T10:51:07+03:00" > Tue Jun 01, 2021< / time > by Alan Orth in
2021-07-07 15:30:06 +02:00
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
2021-07-20 10:05:03 +02:00
< h2 id = "2021-06-01" > 2021-06-01< / h2 >
2021-07-07 15:30:06 +02:00
< ul >
2021-07-20 10:05:03 +02:00
< 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’ 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’ t running< / li >
< li > I simply started it and AReS was running again:< / li >
< / ul >
< / li >
2021-07-07 15:30:06 +02:00
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-06/' > Read more →< / a >
< / article >
2021-05-02 18:55:06 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-05/" > May, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-05-02T09:50:54+03:00" > Sun May 02, 2021< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< 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 > “ RI/1.0” , 1337< / li >
< li > “ Microsoft Office Word 2014” , 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… as that’ s an actual user… < / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-05/' > Read more →< / a >
< / article >
2021-04-05 18:36:44 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-04/" > April, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-04-01T09:50:54+03:00" > Thu Apr 01, 2021< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< h2 id = "2021-04-01" > 2021-04-01< / h2 >
< ul >
< li > I wrote a script to query Sherpa’ s API for our ISSNs: < code > sherpa-issn-lookup.py< / code >
< ul >
< li > I’ 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’ 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-04/' > Read more →< / a >
< / article >
2021-03-04 21:46:05 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-03/" > March, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-03-01T10:13:54+02:00" > Mon Mar 01, 2021< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< h2 id = "2021-03-01" > 2021-03-01< / h2 >
< ul >
< li > Discuss some OpenRXV issues with Abdullah from CodeObia
< ul >
< li > He’ 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-03/' > Read more →< / a >
< / article >
2021-04-01 08:49:08 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/" > CGSpace CG Core v2 Migration< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-02-21T13:27:35+02:00" > Sun Feb 21, 2021< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< span class = "fas fa-tag" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/tags/migration/" rel = "tag" > Migration< / a >
< / p >
< / header >
< 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/' > Read more →< / a >
< / article >
2021-02-01 11:28:54 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-02/" > February, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-02-01T10:13:54+02:00" > Mon Feb 01, 2021< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< h2 id = "2021-02-01" > 2021-02-01< / h2 >
< ul >
2021-02-04 16:28:20 +01:00
< 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 >
2021-02-01 11:28:54 +01:00
< li > Check the results of the AReS harvesting from last night:< / li >
< / ul >
2021-09-13 15:21:16 +02:00
< pre tabindex = "0" > < code class = "language-console" data-lang = "console" > $ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*& pretty'
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{
" count" : 100875,
" _shards" : {
" total" : 1,
" successful" : 1,
" skipped" : 0,
" failed" : 0
}
}
< / code > < / pre >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-02/' > Read more →< / a >
< / article >
2018-02-11 17:28:23 +01:00
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< a class = "btn btn-outline-primary disabled" href = "#" role = "button" aria-disabled = "true" > Previous page< / a >
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2018-04-23 17:09:26 +02:00
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< h4 > Recent Posts< / h4 >
< ol class = "list-unstyled" >
2021-10-04 18:40:13 +02:00
< li > < a href = "/cgspace-notes/2021-10/" > October, 2021< / a > < / li >
2021-09-02 16:21:48 +02:00
< li > < a href = "/cgspace-notes/2021-09/" > September, 2021< / a > < / li >
2021-08-01 15:19:05 +02:00
< li > < a href = "/cgspace-notes/2021-08/" > August, 2021< / a > < / li >
2021-07-20 10:05:03 +02:00
< li > < a href = "/cgspace-notes/2021-07/" > July, 2021< / a > < / li >
2021-06-03 20:54:49 +02:00
2021-07-20 10:05:03 +02:00
< li > < a href = "/cgspace-notes/2021-06/" > June, 2021< / a > < / li >
2021-07-07 15:30:06 +02:00
2018-02-11 17:28:23 +01:00
< / ol >
< / section >
< section class = "sidebar-module" >
< h4 > Links< / h4 >
< ol class = "list-unstyled" >
< li > < a href = "https://cgspace.cgiar.org" > CGSpace< / a > < / li >
< li > < a href = "https://dspacetest.cgiar.org" > DSpace Test< / a > < / li >
< li > < a href = "https://github.com/ilri/DSpace" > CGSpace @ GitHub< / a > < / li >
< / ol >
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2019-10-11 10:19:42 +02:00
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2018-02-11 17:28:23 +01:00
Blog template created by < a href = "https://twitter.com/mdo" > @mdo< / a > , ported to Hugo by < a href = 'https://twitter.com/mralanorth' > @mralanorth< / a > .
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