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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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2024-11-19 08:40:23 +01:00
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2022-05/" > May, 2022< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2022-05-04T09:13:39+03:00" > Wed May 04, 2022< / 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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< / header >
< 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’ 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’ 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2022-05/' > Read more →< / a >
< / article >
2024-10-03 10:51:44 +02:00
< article class = "blog-post" >
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2022-04/" > April, 2022< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2022-04-01T10:53:39+03:00" > Fri Apr 01, 2022< / 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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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’ 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.
< a href = 'https://alanorth.github.io/cgspace-notes/2022-04/' > Read more →< / a >
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2024-09-09 09:20:09 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2022-03/" > March, 2022< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2022-03-01T16:46:54+03:00" > Tue Mar 01, 2022< / 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 = "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 > /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" > ' fuuu' < / 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 > /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 > /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
< / span > < / span > < / code > < / pre > < / div >
< a href = 'https://alanorth.github.io/cgspace-notes/2022-03/' > Read more →< / a >
< / article >
2024-08-28 10:35:05 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2022-02/" > February, 2022< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2022-02-01T14:06:54+02:00" > Tue Feb 01, 2022< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2022-02/' > Read more →< / a >
< / article >
2024-07-02 10:12:03 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2022-01/" > January, 2022< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2022-01-01T15:20:54+02:00" > Sat Jan 01, 2022< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< h2 id = "2022-01-01" > 2022-01-01< / h2 >
< ul >
< li > Start a full harvest on AReS< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2022-01/' > Read more →< / a >
< / article >
2024-06-03 16:31:03 +02:00
< article class = "blog-post" >
< header >
< 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 >
< / p >
< / header >
< 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-12/' > Read more →< / a >
< / article >
2024-05-01 16:10:05 +02:00
< article class = "blog-post" >
< header >
< 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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< / header >
< 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" > ' 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 >
< / article >
2024-04-04 09:23:49 +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 = "/categories/notes/" rel = "category tag" > Notes< / a >
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< / 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 >
< 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 >
< / article >
2024-03-04 08:02:14 +01:00
< 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 = "/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 >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2021-09/' > Read more →< / a >
< / article >
2024-02-06 09:45:02 +01:00
< 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 = "/categories/notes/" rel = "category tag" > Notes< / a >
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< / 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 >
< 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 >
< / article >
2023-07-04 07:03:36 +02:00
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< h4 > Recent Posts< / h4 >
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2024-11-19 08:40:23 +01:00
< li > < a href = "/cgspace-notes/2024-11/" > November, 2024< / a > < / li >
2024-10-03 10:51:44 +02:00
< li > < a href = "/cgspace-notes/2024-10/" > October, 2024< / a > < / li >
2024-09-09 09:20:09 +02:00
< li > < a href = "/cgspace-notes/2024-09/" > September, 2024< / a > < / li >
2024-08-28 10:35:05 +02:00
< li > < a href = "/cgspace-notes/2024-08/" > August, 2024< / a > < / li >
2024-07-02 10:12:03 +02:00
< li > < a href = "/cgspace-notes/2024-07/" > July, 2024< / a > < / li >
2023-07-04 07:03:36 +02:00
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< 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 >
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