CGSpace Notes

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

2021-07-01

• Export another list of ALL subjects on CGSpace, including AGROVOC and non-AGROVOC for Enrico:

localhost/dspace63= > \COPY (SELECT DISTINCT LOWER(text_value) AS subject, count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (119, 120, 127, 122, 128, 125, 135, 203, 208, 210, 215, 123, 236, 242, 187) GROUP BY subject ORDER BY count DESC) to /tmp/2021-07-01-all-subjects.csv WITH CSV HEADER;
COPY 20994

2021-06-01

• IWMI notified me that AReS was down with an HTTP 502 error
  • Looking at UptimeRobot I see it has been down for 33 hours, but I never got a notification
  • I don’t see anything in the Elasticsearch container logs, or the systemd journal on the host, but I notice that the angular_nginx container isn’t running
  • I simply started it and AReS was running again: