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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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2021-09-02 16:21:48 +02:00
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< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2020-03/" > March, 2020< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2020-03-02T12:31:30+02:00" > Mon Mar 02, 2020< / 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 = "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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2020-03/' > 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/2020-02/" > February, 2020< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2020-02-02T11:56:30+02:00" > Sun Feb 02, 2020< / 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 = "2020-02-02" > 2020-02-02< / h2 >
< ul >
< li > Continue working on porting CGSpace’ 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2020-02/' > Read more →< / a >
< / article >
2021-07-07 15:30:06 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2020-01/" > January, 2020< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2020-01-06T10:48:30+02:00" > Mon Jan 06, 2020< / 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 = "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://handle.hdl.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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2020-01/' > Read more →< / a >
< / article >
2021-06-03 20:54:49 +02:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2019-12/" > December, 2019< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2019-12-01T11:22:30+02:00" > Sun Dec 01, 2019< / 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 = "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 ‘ ^rc’ | awk ‘ {print $2}’ | 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 > < code > # apt update & & apt full-upgrade
# apt-get autoremove & & apt-get autoclean
# dpkg -C
# reboot
< / code > < / pre >
< a href = 'https://alanorth.github.io/cgspace-notes/2019-12/' > 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/2019-11/" > November, 2019< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2019-11-04T12:20:30+02:00" > Mon Nov 04, 2019< / 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 = "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 > < code > # zcat --force /var/log/nginx/*access.log.*.gz | grep -cE " [0-9]{1,2}/Oct/2019"
4671942
# zcat --force /var/log/nginx/{rest,oai,statistics}.log.*.gz | grep -cE " [0-9]{1,2}/Oct/2019"
1277694
< / code > < / pre > < ul >
< li > So 4.6 million from XMLUI and another 1.2 million from API requests< / li >
< li > Let’ s see how many of the REST API requests were for bitstreams (because they are counted in Solr stats):< / li >
< / ul >
< pre > < code > # zcat --force /var/log/nginx/rest.log.*.gz | grep -c -E " [0-9]{1,2}/Oct/2019"
1183456
# zcat --force /var/log/nginx/rest.log.*.gz | grep -E " [0-9]{1,2}/Oct/2019" | grep -c -E " /rest/bitstreams"
106781
< / code > < / pre >
< a href = 'https://alanorth.github.io/cgspace-notes/2019-11/' > 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/2019-10/" > October, 2019< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2019-10-01T13:20:51+03:00" > Tue Oct 01, 2019< / 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 >
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’ s “ unneccesary Unicode” fix: $ csvcut -c 'id,dc.
< a href = 'https://alanorth.github.io/cgspace-notes/2019-10/' > 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/2019-09/" > September, 2019< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2019-09-01T10:17:51+03:00" > Sun Sep 01, 2019< / 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 = "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 > < code > # zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -E " 01/Sep/2019:0" | awk '{print $1}' | 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 " 01/Sep/2019:0" | awk '{print $1}' | 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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2019-09/' > 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/2019-08/" > August, 2019< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2019-08-03T12:39:51+03:00" > Sat Aug 03, 2019< / 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 = "2019-08-03" > 2019-08-03< / h2 >
< ul >
< li > Look at Bioversity’ 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… < / 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… < / li >
< li > After rebooting, all statistics cores were loaded… wow, that’ s lucky.< / li >
< / ul >
< / li >
< li > Run system updates on DSpace Test (linode19) and reboot it< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2019-08/' > Read more →< / a >
< / article >
2021-01-03 09:15:24 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2019-07/" > July, 2019< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2019-07-01T12:13:51+03:00" > Mon Jul 01, 2019< / 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 = "2019-07-01" > 2019-07-01< / h2 >
< ul >
< li > Create an “ AfricaRice books and book chapters” collection on CGSpace for AfricaRice< / li >
< li > Last month Sisay asked why the following “ most popular” 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&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&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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2019-07/' > Read more →< / a >
< / article >
2020-12-01 18:15:48 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2019-06/" > June, 2019< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2019-06-02T10:57:51+03:00" > Sun Jun 02, 2019< / 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 = "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 >
< a href = 'https://alanorth.github.io/cgspace-notes/2019-06/' > Read more →< / a >
< / article >
2018-02-11 17:28:23 +01:00
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< h4 > Recent Posts< / h4 >
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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
2021-05-02 18:55:06 +02:00
< li > < a href = "/cgspace-notes/2021-05/" > May, 2021< / a > < / li >
2018-02-11 17:28:23 +01:00
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< / 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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