CGSpace Notes

2020-01-06

• Open a ticket with Atmire to request a quote for the upgrade to DSpace 6
• Last week Altmetric responded about the item that had a lower score than than its DOI
  • The score is now linked to the DOI
  • Another item that had the same problem in 2019 has now also linked to the score for its DOI
  • Another item that had the same problem in 2019 has also been fixed

2020-01-07

• Peter Ballantyne highlighted one more WLE item that is missing the Altmetric score that its DOI has
  • The DOI has a score of 259, but the Handle has no score at all
  • I tweeted the CGSpace repository link

2019-12-01

• Upgrade CGSpace (linode18) to Ubuntu 18.04:
  • Check any packages that have residual configs and purge them:
  • # dpkg -l | grep -E ‘^rc’ | awk ‘{print $2}’ | xargs dpkg -P
  • Make sure all packages are up to date and the package manager is up to date, then reboot:

# apt update && apt full-upgrade
# apt-get autoremove && apt-get autoclean
# dpkg -C
# reboot

2019-11-04

• Peter noticed that there were 5.2 million hits on CGSpace in 2019-10 according to the Atmire usage statistics
  • I looked in the nginx logs and see 4.6 million in the access logs, and 1.2 million in the API logs:

# 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

• So 4.6 million from XMLUI and another 1.2 million from API requests
• Let’s see how many of the REST API requests were for bitstreams (because they are counted in Solr stats):

# 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

2019-09-01

• Linode emailed to say that CGSpace (linode18) had a high rate of outbound traffic for several hours this morning
• Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:

# 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

2019-08-03

• 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…

2019-08-04

• Deploy ORCID identifier updates requested by Bioversity to CGSpace
• Run system updates on CGSpace (linode18) and reboot it
  • Before updating it I checked Solr and verified that all statistics cores were loaded properly…
  • After rebooting, all statistics cores were loaded… wow, that’s lucky.
• Run system updates on DSpace Test (linode19) and reboot it

2019-07-01

• Create an “AfricaRice books and book chapters” collection on CGSpace for AfricaRice
• 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:
  • DSpace Test
  • CGSpace
• Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community

2019-06-02

• Merge the Solr filterCache and XMLUI ISI journal changes to the 5_x-prod branch and deploy on CGSpace
• Run system updates on CGSpace (linode18) and reboot it

2019-06-03

• Skype with Marie-Angélique and Abenet about CG Core v2

2019-05-01

• Help CCAFS with regenerating some item thumbnails after they uploaded new PDFs to some items on CGSpace
• A user on the dspace-tech mailing list offered some suggestions for troubleshooting the problem with the inability to delete certain items
  • Apparently if the item is in the workflowitem table it is submitted to a workflow
  • And if it is in the workspaceitem table it is in the pre-submitted state
• The item seems to be in a pre-submitted state, so I tried to delete it from there:

dspace=# DELETE FROM workspaceitem WHERE item_id=74648;
DELETE 1

• But after this I tried to delete the item from the XMLUI and it is still present…

2019-04-01

• Meeting with AgroKnow to discuss CGSpace, ILRI data, AReS, GARDIAN, etc
  • They asked if we had plans to enable RDF support in CGSpace
• There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today
  • I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!

# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep 'Spore-192-EN-web.pdf' | grep -E '(18.196.196.108|18.195.78.144|18.195.218.6)' | awk '{print $9}' | sort | uniq -c | sort -n | tail -n 5
   4432 200

• In the last two weeks there have been 47,000 downloads of this same exact PDF by these three IP addresses
• Apply country and region corrections and deletions on DSpace Test and CGSpace:

$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-9-countries.csv -db dspace -u dspace -p 'fuuu' -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 'fuuu' -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 'fuuu' -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 'fuuu' -m 231 -f cg.coverage.region -d