CGSpace Notes

Documenting day-to-day work on the CGSpace repository.

November, 2021

in  Notes

2021-11-02

  • I experimented with manually sharding the Solr statistics on DSpace Test
  • First I exported all the 2019 stats from CGSpace:
$ ./run.sh -s http://localhost:8081/solr/statistics -f 'time:2019-*' -a export -o statistics-2019.json -k uid
$ zstd statistics-2019.json

$ mkdir -p /home/dspacetest.cgiar.org/solr/statistics-2019/data
# create core in Solr admin
$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>time:2019-*</query></delete>"
$ ./run.sh -s http://localhost:8081/solr/statistics-2019 -a import -o statistics-2019.json -k uid
  • The key thing above is that you create the core in the Solr admin UI, but the data directory must already exist so you have to do that first in the file system
  • I restarted the server after the import was done to see if the cores would come back up OK
    • I remember last time I tried this the manually created statistics cores didn’t come back up after I rebooted, but this time they did

2021-11-03

  • While inspecting the stats for the new statistics-2019 shard on DSpace Test I noticed that I can’t find any stats via the DSpace Statistics API for an item that should have some
    • I checked on CGSpace’s and I can’t find them there either, but I see them in Solr when I query in the admin UI
    • I need to debug that, but it doesn’t seem to be related to the sharding…

2021-11-04

  • I spent a little bit of time debugging the Solr bug with the statistics-2019 shard but couldn’t reproduce it for the few items I tested
    • So that’s good, it seems the sharding worked
  • Linode alerted me to high CPU usage on CGSpace (linode18) yesterday
    • Looking at the Solr hits from yesterday I see 91.213.50.11 making 2,300 requests
    • According to AbuseIPDB.com this is owned by Registrarus LLC (registrarus.ru) and it has been reported for malicious activity by several users
    • The ASN is 50340 (SELECTEL-MSK, RU)
    • They are attempting SQL injection:
91.213.50.11 - - [03/Nov/2021:06:47:20 +0100] "HEAD /bitstream/handle/10568/106239/U19ArtSimonikovaChromosomeInthomNodev.pdf?sequence=1%60%20WHERE%206158%3D6158%20AND%204894%3D4741--%20kIlq&isAllowed=y HTTP/1.1" 200 0 "https://cgspace.cgiar.org:443/bitstream/handle/10568/106239/U19ArtSimonikovaChromosomeInthomNodev.pdf" "Mozilla/5.0 (X11; U; Linux i686; en-CA; rv:1.8.0.10) Gecko/20070223 Fedora/1.5.0.10-1.fc5 Firefox/1.5.0.10"
  • Another is in China, and they grabbed 1,200 PDFs from the REST API in under an hour:
# zgrep 222.129.53.160 /var/log/nginx/rest.log.2.gz | wc -l
1178
  • I will continue to split the Solr statistics back into year-shards on DSpace Test (linode26)
    • Today I did all 2018 stats…
    • I want to see if there is a noticeable change in JVM memory, Solr response time, etc

2021-11-07

  • Update all Docker containers on AReS and rebuild OpenRXV:
$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
$ docker-compose build
  • Then restart the server and start a fresh harvest
  • Continue splitting the Solr statistics into yearly shards on DSpace Test (doing 2017, 2016, 2015, and 2014 today)
  • Several users wrote to me last week to say that workflow emails haven’t been working since 2021-10-21 or so
    • I did a test on CGSpace and it’s indeed broken:
$ dspace test-email

About to send test email:
 - To: fuuuu
 - Subject: DSpace test email
 - Server: smtp.office365.com

Error sending email:
 - Error: javax.mail.SendFailedException: Send failure (javax.mail.AuthenticationFailedException: 535 5.7.139 Authentication unsuccessful, the user credentials were incorrect. [AM5PR0701CA0005.eurprd07.prod.outlook.com]
)

Please see the DSpace documentation for assistance.
  • I sent a message to ILRI ICT to ask them to check the account/password
  • I want to do one last test of the Elasticsearch updates on OpenRXV so I got a snapshot of the latest Elasticsearch volume used on the production AReS instance:
# tar czf openrxv_esData_7.tar.xz /var/lib/docker/volumes/openrxv_esData_7
  • Then on my local server:
$ mv ~/.local/share/containers/storage/volumes/openrxv_esData_7/ ~/.local/share/containers/storage/volumes/openrxv_esData_7.2021-11-07.bak
$ tar xf /tmp/openrxv_esData_7.tar.xz -C ~/.local/share/containers/storage/volumes --strip-components=4
$ find ~/.local/share/containers/storage/volumes/openrxv_esData_7 -type f -exec chmod 660 {} \;
$ find ~/.local/share/containers/storage/volumes/openrxv_esData_7 -type d -exec chmod 770 {} \;
# copy backend/data to /tmp for the repository setup/layout
$ rsync -av --partial --progress --delete provisioning@ares:/tmp/data/ backend/data
  • This seems to work: all items, stats, and repository setup/layout are OK
  • I merged my Elasticsearch pull request from last month into OpenRXV

2021-11-08

  • File an issue for the Angular flash of unstyled content on DSpace 7
  • Help Udana from IWMI with a question about CGSpace statistics
    • He found conflicting numbers when using the community and collection modes in Content and Usage Analysis
    • I sent him more numbers directly from the DSpace Statistics API