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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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2023-08-04 17:05:44 +02:00
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-12/" > December, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-12-01T16:07:07+02:00" > Wed Dec 01, 2021< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2021-12-01" > 2021-12-01< / h2 >
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< 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-12/' > Read more →< / a >
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2023-07-04 07:03:36 +02:00
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2021-11/" > November, 2021< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2021-11-02T22:27:07+02:00" > Tue Nov 02, 2021< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2021-11-02" > 2021-11-02< / h2 >
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< li > I experimented with manually sharding the Solr statistics on DSpace Test< / li >
< li > First I exported all the 2019 stats from CGSpace:< / li >
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< 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" > ' time:2019-*' < / 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-11/' > Read more →< / a >
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< 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 = "/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2021-10-01" > 2021-10-01< / h2 >
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< 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= > \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;
< / span > < / span > < span style = "display:flex;" > < span > $ csvcut -c < span style = "color:#ae81ff" > 1< / span > /tmp/2021-10-01-affiliations.csv | sed 1d > /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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-10/' > Read more →< / a >
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< 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 = "/categories/notes/" rel = "category tag" > Notes< / a >
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< 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 >
< 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 >
< / 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 >
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< a href = 'https://alanorth.github.io/cgspace-notes/2021-09/' > Read more →< / a >
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< 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 = "/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2021-08-01" > 2021-08-01< / h2 >
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< li > Update Docker images on AReS server (linode20) and reboot the server:< / li >
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< 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" > ' s/ \+/:/g' < / 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-08/' > Read more →< / a >
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< 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
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2021-07-01" > 2021-07-01< / h2 >
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< 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= > \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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-07/' > Read more →< / a >
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< 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
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2021-06-01" > 2021-06-01< / h2 >
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< 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 >
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< a href = 'https://alanorth.github.io/cgspace-notes/2021-06/' > Read more →< / a >
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< 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 = "/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2021-05-01" > 2021-05-01< / h2 >
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< 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 >
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< 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 = "/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2021-04-01" > 2021-04-01< / h2 >
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< 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 >
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< / 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 >
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< a href = 'https://alanorth.github.io/cgspace-notes/2021-04/' > Read more →< / a >
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< 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 = "/categories/notes/" rel = "category tag" > Notes< / a >
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< h2 id = "2021-03-01" > 2021-03-01< / h2 >
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< li > Discuss some OpenRXV issues with Abdullah from CodeObia
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< 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 >
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< a href = 'https://alanorth.github.io/cgspace-notes/2021-03/' > Read more →< / a >
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2023-08-04 17:05:44 +02:00
< li > < a href = "/cgspace-notes/2023-08/" > August, 2023< / a > < / li >
2023-07-04 07:03:36 +02:00
< li > < a href = "/cgspace-notes/2023-07/" > July, 2023< / a > < / li >
< li > < a href = "/cgspace-notes/2023-06/" > June, 2023< / a > < / li >
< li > < a href = "/cgspace-notes/2023-05/" > May, 2023< / a > < / li >
< li > < a href = "/cgspace-notes/2023-04/" > April, 2023< / a > < / li >
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< h4 > Links< / h4 >
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< 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 >
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