CGSpace Notes

2020-05-02

• Peter said that CTA is having problems submitting an item to CGSpace
  • Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in ‘idle in transaction’ and ‘waiting for lock’ state are increasing again
  • I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)

2020-04-02

• Maria asked me to update Charles Staver’s ORCID iD in the submission template and on CGSpace, as his name was lower case before, and now he has corrected it
  • I updated the fifty-eight existing items on CGSpace
• Looking into the items Udana had asked about last week that were missing Altmetric donuts:
  • The first is still missing its DOI, so I added it and tweeted its handle (after a few hours there was a donut with score 222)
  • The second item now has a donut with score 2 since I tweeted its handle last week
  • The third item now has a donut with score 1 since I tweeted it last week
• On the same note, the one item Abenet pointed out last week now has a donut with score of 104 after I tweeted it last week

2020-03-02

• Update dspace-statistics-api for DSpace 6+ UUIDs
  • Tag version 1.2.0 on GitHub
• Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased SolrUpgradePre6xStatistics.java
  • You need to download this into the DSpace 6.x source and compile it

2020-02-02

• Continue working on porting CGSpace’s DSpace 5 code to DSpace 6.3 that I started yesterday
  • Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database
  • I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks
  • Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff
  • The code finally builds and runs with a fresh install

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