CGSpace Notes

2022-05-04

• 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:
  • 18.207.136.176
  • 185.189.36.248
  • 50.118.223.78
  • 52.70.76.123
  • 3.236.10.11
• Looking at the Solr statistics for 2022-04
  • 52.191.137.59 is Microsoft, but they are using a normal user agent and making tens of thousands of requests
  • 64.39.98.62 is owned by Qualys, and all their requests are probing for /etc/passwd etc
  • 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
  • 157.55.39.159 is owned by Microsoft and identifies as bingbot so I don’t know why its requests were logged in Solr
  • 52.233.67.176 is owned by Microsoft and uses a normal user agent, but making excessive automated HTTP requests
  • 157.55.39.144 is owned by Microsoft and uses a normal user agent, but making excessive automated HTTP requests
  • 207.46.13.177 is owned by Microsoft and identifies as bingbot so I don’t know why its requests were logged in Solr
  • If I query Solr for time:2022-04* AND dns:*msnbot* AND dns:*.msn.com. I see a handful of IPs that made 41,000 requests
• I purged 93,974 hits from these IPs using my check-spider-ip-hits.sh script

2022-03-01

• Send Gaia the last batch of potential duplicates for items 701 to 980:

$ csvcut -c id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4.csv
$ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p 'fuuu' -o /tmp/2022-03-01-tac-batch4-701-980.csv
$ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4-filenames.csv
$ 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

2022-02-01

• Meeting with Peter and Abenet about CGSpace in the One CGIAR
  • We agreed to buy $5,000 worth of credits from Atmire for future upgrades
  • We agreed to move CRPs and non-CGIAR communities off the home page, as well as some other things for the CGIAR System Organization
  • We agreed to make a Discovery facet for CGIAR Action Areas above the existing CGIAR Impact Areas one
  • We agreed to try to do more alignment of affiliations/funders with ROR

2022-01-01

• Start a full harvest on AReS

2021-12-01

• Atmire merged some changes I had submitted to the COUNTER-Robots project
• I updated our local spider user agents and then re-ran the list with my check-spider-hits.sh script on CGSpace:

$ ./ilri/check-spider-hits.sh -f /tmp/agents -p  
Purging 1989 hits from The Knowledge AI in statistics
Purging 1235 hits from MaCoCu in statistics
Purging 455 hits from WhatsApp in statistics

Total number of bot hits purged: 3679

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

2021-10-01

• Export all affiliations on CGSpace and run them against the latest RoR data dump:

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;
$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d > /tmp/2021-10-01-affiliations.txt
$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
ations-matching.csv
$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l 
1879
$ wc -l /tmp/2021-10-01-affiliations.txt 
7100 /tmp/2021-10-01-affiliations.txt

• So we have 1879/7100 (26.46%) matching already

2021-09-02

• Troubleshooting the missing Altmetric scores on AReS
  • Turns out that I didn’t actually fix them last month because the check for content.altmetric still exists, and I can’t access the DOIs using _h.source.DOI for some reason
  • I can access all other kinds of item metadata using the Elasticsearch label, but not DOI!!!
  • I will change DOI to tomato in the repository setup and start a re-harvest… I need to see if this is some kind of reserved word or something…
  • Even as tomato I can’t access that field as _h.source.tomato in Angular, but it does work as a filter source… sigh
• I’m having problems using the OpenRXV API
  • The syntax Moayad showed me last month doesn’t seem to honor the search query properly…

2021-08-01

• Update Docker images on AReS server (linode20) and reboot the server:

# docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull

• I decided to upgrade linode20 from Ubuntu 18.04 to 20.04