June, 2024

Mon Jun 03, 2024 in Notes

2024-06-03

Working on IFPRI datasets
- I noticed the licenses were missing from Nilam’s original file so I found a way to check Dataverse’s API for a persistent identifier
- We have both Handles and DOIs for these datasets, both from Harvard’s Dataverse

I used this GREL in OpenRefine to create a new column based on URLs using the DOI (uppercasing the DOI for Dataverse):

"https://dataverse.harvard.edu/api/datasets/export?exporter=dataverse_json&persistentId=doi:" + value.split('https://doi.org/')[-1].toUppercase()

Then I was able to extract the license text from the JSON response using:

value.parseJson()['datasetVersion']['termsOfUse']

Similar for the Handle…

2024-06-04

Some Dataverse entries have the license in ['datasetVersion']['license'] instead…
I finalized cleaning the 722 IFPRI datasets and uploaded them to CGSpace

2024-06-14

Minor cleanups on IFPRI’s 2016–2019 batch migration file
- I will start with duplicates on unique identifiers like DOIs

2026-06-18

Merge and upload metadata for duplicates in IFPRI’s 2016–2019 set:
- 144 exact match on CGSpace via DOI, type, and date
- 32 with CGSpace handles
- I also spent some time converting the ilri/post_bitstreams.py script to use the DSpace 7 REST API via dspace-rest-client
- There are 28 PDFs specified for these 176 duplicates, and a handful of them do not already exist on CGSpace so I will upload them

2024-06-19

Spent some time checking the remaining 3312 IFPRI 2016–2019 migration set for duplicates on CGSpace
- There seem to be about 50 exact matches of title, type, and issue date

2024-06-20

Finalize merging and uploading metadata for 48 duplicates from the IFPRI 2016–2019 migration set
Heavy load on both CGSpace and DSpace 7 Test this afternoon
- Took me a while to figure out it was due to someone / something hammering /search for a bunch of facets
- The pm2 logs command was more useful than the nginx logs to see the requests at least, for example:

0|dspace-ui  | GET /search?f.sdg=SDG%2013%20-%20Climate%20action,equals&spc.page=1&f.accessRights=Open%20Access,equals&f.dateIssued.min=2023&f.dateIssued.max=2024&f.country=Colombia,equals&f.subject=climate%20change,equals&f.region=Latin%20America%20and%20the%20Caribbean,equals&f.publisher=CGIAR%20FOCUS%20Climate%20Security,equals - - ms - -
1|dspace-ui  | GET /search?f.accessRights=Open%20Access,equals&spc.page=1&f.sponsorship=CGIAR%20Trust%20Fund,equals&f.impactArea=Climate%20adaptation%20and%20mitigation,equals&f.region=Eastern%20Africa,equals&f.publisher=International%20Institute%20of%20Tropical%20Agriculture,equals - - ms - -
3|dspace-ui  | GET /search?f.sdg=SDG%2013%20-%20Climate%20action,equals&f.sdg=SDG%2012%20-%20Responsible%20consumption%20and%20production,equals&spc.page=1&f.affiliation=CGIAR%20Research%20Program%20on%20Climate%20Change,%20Agriculture%20and%20Food%20Security,equals&f.affiliation=Alliance%20of%20Bioversity%20International%20and%20CIAT,equals&f.dateIssued.min=2020&f.dateIssued.max=2021&f.impactArea=Environmental%20health%20and%20biodiversity,equals - - ms - -

Still difficult to find the client, because the logs are all coming from Angular’s user agent and IP
- I changed the nginx logging to use the X-Forwarded-For header, as the default combined log format uses $remote_addr by default, which is only accurate if the request doesn’t come from Angular (ie directly to the API)
- From what I can see now the IPs are all coming from Huawei Cloud and Tencent
- The ASNs are AS136907 (Huawei) and AS132203 (Tencent)
- For now I will just add those to the list of bot networks

2024-06-21

Update the nginx logging to use nginx’s real_ip module to log the correct client IP
- I think this means we will start sending ‘bot’ to the Angular / Express frontend because bot IPs will be properly classified now…
- I will have to re-work or at least re-think that nginx configuration for requests going to the frontend because the proposed fix in https://github.com/DSpace/dspace-angular/issues/2902 is to pass on the client’s user-agent
Then I updated the list of bot networks:

$ wget https://asn.ipinfo.app/api/text/list/AS12876 \
     https://asn.ipinfo.app/api/text/list/AS132203 \
     https://asn.ipinfo.app/api/text/list/AS13238 \
     https://asn.ipinfo.app/api/text/list/AS136907 \
     https://asn.ipinfo.app/api/text/list/AS14061 \
     https://asn.ipinfo.app/api/text/list/AS14618 \
     https://asn.ipinfo.app/api/text/list/AS16276 \
     https://asn.ipinfo.app/api/text/list/AS16509 \
     https://asn.ipinfo.app/api/text/list/AS203020 \
     https://asn.ipinfo.app/api/text/list/AS204287 \
     https://asn.ipinfo.app/api/text/list/AS21859 \
     https://asn.ipinfo.app/api/text/list/AS23576 \
     https://asn.ipinfo.app/api/text/list/AS24940 \
     https://asn.ipinfo.app/api/text/list/AS396982 \
     https://asn.ipinfo.app/api/text/list/AS45102 \
     https://asn.ipinfo.app/api/text/list/AS50245 \
     https://asn.ipinfo.app/api/text/list/AS55286 \
     https://asn.ipinfo.app/api/text/list/AS6939 \
     https://asn.ipinfo.app/api/text/list/AS8075
$ cat AS* | ~/go/bin/mapcidr -a > /tmp/networks.txt
$ wc -l /tmp/networks.txt
8675 /tmp/networks.txt

Update list of ORCID identifiers with new ones from Alliance and IFPRI
Finalize uploading the remaining 3,264 items from IFPRI’s 2016–2019 batch migration to CGSpace

2024-06-24

Minor updates to csv-metadata-quality and cgspace-java-helpers to normalize a few more invalid DOI formats

2024-06-25

Work on uploading some missing PDFs from the IFPRI 2016–2019 batch migration

2024-06-26

Did a big cleanup of several thousand journal articles based on metadata from Crossref