CGSpace Notes

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

January, 2024

in  Notes

2024-01-02

  • Work on preparation of new server for DSpace 7 migration
    • I’m not quite sure what we need to do for the Handle server
    • For now I just ran the dspace make-handle-config script and diffed it with the one from DSpace 6
    • I sent the bundle to the Handle admins to make sure it’s OK before we do the migration
  • Continue testing and debugging the cgspace-java-helpers on DSpace 7
  • Work on IFPRI ISNAR archive cleanup

2024-01-03

  • I haven’t heard from the Handle admins so I’m preparing a backup solution using nginx streams
  • This seems to work in my simple tests (this must be outside the http {} block):
stream {
    upstream handle_tcp_9000 {
       server 188.34.177.10:9000;
    }

    server {
        listen 9000;
        proxy_connect_timeout 1s;
        proxy_timeout 3s;
        proxy_pass handle_tcp_9000;
    }
}
  • Here I forwarded a test TCP port 9000 from one server to another and was able to retrieve a test HTML that was running on the target
    • I will have to do TCP and UDP on port 2641, and TCP/HTTP on port 8000.
  • I did some more minor work on the IFPRI ISNAR archive
    • I got some PDFs from the UMN AgEcon search and fixed some metadata
    • Then I did some duplicate checking and found five items already on CGSpace

2024-01-04

  • Upload 692 items for the ISNAR archive to CGSpace: https://cgspace.cgiar.org/handle/10568/136192
  • Help Peter proof and upload 252 items from the 2023 Gender conference to CGSpace
  • Meeting with IFPRI to discuss their migration to CGSpace
    • We agreed to add two new fields, one for IFPRI project and one for IFPRI publication ranking
    • Most likely we will use cg.identifier.project as a general field and consolidate other project fields there
    • Not sure which field to use for the publication rank…

2024-01-05

  • Proof and upload 51 items in bulk for IFPRI
  • I did a big cleanup of user groups in anticipation of complaints about slow workflow tasks etc in DSpace 7
    • I removed ILRI editors from all the dozens of CCAFS community and collection groups, and I should do the same for other CRPs since they are closed for two years now

2024-01-06

  • Migrate CGSpace to DSpace 7

2024-01-07

  • High load on the server and UptimeRobot saying the frontend is flapping
    • I noticed tons of logs from pm2 in the systemd journal, so I disabled those in the systemd unit because they are available from pm2’s log directory anyway
    • I also noticed the same for Solr, so I disabled stdout for that systemd unit as well
  • I spent a lot of time bringing back the nginx rate limits we used in DSpace 6 and it seems to have helped
  • I see some client doing weird HEAD requests to search pages:
47.76.35.19 - - [07/Jan/2024:00:00:02 +0100] "HEAD /search/?f.accessRights=Open+Access%2Cequals&f.actionArea=Resilient+Agrifood+Systems%2Cequals&f.author=Burkart%2C+Stefan%2Cequals&f.country=Kenya%2Cequals&f.impactArea=Climate+adaptation+and+mitigation%2Cequals&f.itemtype=Brief%2Cequals&f.publisher=CGIAR+System+Organization%2Cequals&f.region=Asia%2Cequals&f.sdg=SDG+12+-+Responsible+consumption+and+production%2Cequals&f.sponsorship=CGIAR+Trust+Fund%2Cequals&f.subject=environmental+factors%2Cequals&spc.page=1 HTTP/1.1" 499 0 "-" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/74.0.2504.63 Safari/537.36"
  • I will add their network blocks (AS45102) and regenerate my list of bot networks:
$ wget https://asn.ipinfo.app/api/text/list/AS16276 \
     https://asn.ipinfo.app/api/text/list/AS23576 \
     https://asn.ipinfo.app/api/text/list/AS24940 \
     https://asn.ipinfo.app/api/text/list/AS13238 \
     https://asn.ipinfo.app/api/text/list/AS14061 \
     https://asn.ipinfo.app/api/text/list/AS12876 \
     https://asn.ipinfo.app/api/text/list/AS55286 \
     https://asn.ipinfo.app/api/text/list/AS203020 \
     https://asn.ipinfo.app/api/text/list/AS204287 \
     https://asn.ipinfo.app/api/text/list/AS50245 \
     https://asn.ipinfo.app/api/text/list/AS6939 \
     https://asn.ipinfo.app/api/text/list/AS45102 \
     https://asn.ipinfo.app/api/text/list/AS21859
$ cat AS* | sort | uniq | wc -l
4897
$ cat AS* | ~/go/bin/mapcidr -a > /tmp/networks.txt
$ wc -l /tmp/networks.txt
2017 /tmp/networks.txt
  • I’m surprised to see the number of networks reduced from my current ones… hmmm.
  • I will also update my list of Bing networks:
$ ./ilri/bing-networks-to-ips.sh
$ ~/go/bin/mapcidr -a < /tmp/bing-ips.txt > /tmp/bing-networks.txt
$ wc -l /tmp/bing-networks.txt
250 /tmp/bing-networks.txt

2024-01-08

  • Export list of publishers for Peter to select some amount to use as a controlled vocabulary:
localhost/dspace7= ☘ \COPY (SELECT DISTINCT text_value AS "dcterms.publisher", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id = 178 GROUP BY "dcterms.publisher" ORDER BY count DESC) to /tmp/2024-01-publishers.csv WITH CSV HEADER;
COPY 4332
  • Address some feedback on DSpace 7 from users, including fileing some issues on GitHub
  • The Alliance TIP team was having issues posting to one collection via the legacy DSpace 6 REST API
    • In the DSpace logs I see the same issue that they had last month:
ERROR unknown unknown org.dspace.rest.Resource @ Something get wrong. Aborting context in finally statement.

2024-01-09

  • I restarted Tomcat to see if it helps the REST issue
  • After talking with Peter about publishers we decided to get a clean list of the top ~100 publishers and then make sure all CGIAR centers, Initiatives, and Impact Platforms are there as well
    • I exported a list from PostgreSQL and then filtered by count > 40 in OpenRefine and then extracted the metadata values:
$ csvcut -c dcterms.publisher ~/Downloads/2024-01-09-publishers4.csv | sed -e 1d -e 's/"//g' > /tmp/top-publishers.txt
  • Export a list of ORCID identifiers from PostgreSQL to look them up on ORCID and update our controlled vocabulary:
localhost/dspace7= ☘ \COPY (SELECT DISTINCT(text_value) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=247) to /tmp/2024-01-09-orcid-identifiers.txt;
localhost/dspace7= ☘ \q
$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml /tmp/2024-01-09-orcid-identifiers.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2024-01-09-orcids.txt
$ ./ilri/resolve_orcids.py -i /tmp/2024-01-09-orcids.txt -o /tmp/2024-01-09-orcids-names.txt -d
  • Then I updated existing ORCID identifiers in CGSpace:
$ ./ilri/update_orcids.py -i /tmp/2024-01-09-orcids-names.txt -db dspace -u dspace -p bahhhh
  • Bizu seems to be having issues due to belonging to too many groups
    • I see some messages from Solr in the DSpace log:
2024-01-09 06:23:35,893 ERROR unknown unknown org.dspace.authorize.AuthorizeServiceImpl @ Failed getting getting community/collection admin status for bahhhhh@cgiar.org The search error is: Error from server at http://localhost:8983/solr/search: org.apache.solr.search.SyntaxError: Cannot parse 'search.resourcetype:Community AND (admin:eef481147-daf3-4fd2-bb8d-e18af8131d8c OR admin:g80199ef9-bcd6-4961-9512-501dea076607 OR admin:g4ac29263-cf0c-48d0-8be7-7f09317d50ec OR admin:g0e594148-a0f6-4f00-970d-6b7812f89540 OR admin:g0265b87a-2183-4357-a971-7a5b0c7add3a OR admin:g371ae807-f014-4305-b4ec-f2a8f6f0dcfa OR admin:gdc5cb27c-4a5a-45c2-b656-a399fded70de OR admin:ge36d0ece-7a52-4925-afeb-6641d6a348cc OR admin:g15dc1173-7ddf-43cf-a89a-77a7f81c4cfc OR admin:gc3a599d3-c758-46cd-9855-c98f6ab58ae4 OR admin:g3d648c3e-58c3-4342-b500-07cba10ba52d OR admin:g82bf5168-65c1-4627-8eb4-724fa0ea51a7 OR admin:ge751e973-697d-419c-b59b-5a5644702874 OR admin:g44dd0a80-c1e6-4274-9be4-9f342d74928c OR admin:g4842f9c2-73ed-476a-a81a-7167d8aa7946 OR admin:g5f279b3f-c2ce-4c75-b151-1de52c1a540e OR admin:ga6df8adc-2e1d-40f2-8f1e-f77796d0eecd OR admin:gfdfc1621-382e-437a-8674-c9007627565c OR admin:g15cd114a-0b89-442b-a1b4-1febb6959571 OR admin:g12aede99-d018-4c00-b4d4-a732541d0017 OR admin:gc59529d7-002a-4216-b2e1-d909afd2d4a9 OR admin:gd0806714-bc13-460d-bedd-121bdd5436a4 OR admin:gce70739a-8820-4d56-b19c-f191855479e4 OR admin:g7d3409eb-81e3-4156-afb1-7f02de22065f OR admin:g54bc009e-2954-4dad-8c30-be6a09dc5093 OR admin:gc5e1d6b7-4603-40d7-852f-6654c159dec9 OR admin:g0046214d-c85b-4f12-a5e6-2f57a2c3abb0 OR admin:g4c7b4fd0-938f-40e9-ab3e-447c317296c1 OR admin:gcfae9b69-d8dd-4cf3-9a4e-d6e31ff68731 OR ... admin:g20f366c0-96c0-4416-ad0b-46884010925f)': too many boolean clauses The search resourceType filter was: search.resourcetype:Community
  • There are 1,805 OR clauses in the full log!
    • We previous had this issue in 2020-01 and 2020-02 with DSpace 5 and DSpace 6
    • At the time the solution was to increase the maxBooleanClauses in Solr and to disable access rights awareness, but I don’t think we want to do the second one now
    • I saw many users of Solr in other applications increasing this to obscenely high numbers, so I think we should be OK to increase it from 1024 to 2048
  • Re-visiting the DSpace user groomer to delete inactive users
    • In 2023-08 I noticed that this was now possible in DSpace 7
    • As a test I tried to delete all users who have been inactive since six years ago (Janury 9, 2018):
$ dspace dsrun org.dspace.eperson.Groomer -a -b 01/09/2018 -d
  • I tested it on DSpace 7 Test and it worked… I am debating running it on CGSpace…
    • I see we have almost 9,000 users:
$ dspace user -L > /tmp/users-before.txt
$ wc -l /tmp/users-before.txt
8943 /tmp/users-before.txt
  • I decided to do the same on CGSpace and it worked without errors
  • I finished working on the controlled vocabulary for publishers

2024-01-10

  • I spent some time deleting old groups on CGSpace
  • I looked into the use of the cg.identifier.ciatproject field and found there are only a handful of uses, with some even seeming to be a mistake:
localhost/dspace7= ☘ SELECT DISTINCT text_value AS "cg.identifier.ciatproject", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata
_field_id = 232 GROUP BY "cg.identifier.ciatproject" ORDER BY count DESC;
 cg.identifier.ciatproject │ count
───────────────────────────┼───────
 D145                      │     4
 LAM_LivestockPlus         │     2
 A215                      │     1
 A217                      │     1
 A220                      │     1
 A223                      │     1
 A224                      │     1
 A227                      │     1
 A229                      │     1
 A230                      │     1
 CLIMATE CHANGE MITIGATION │     1
 LIVESTOCK                 │     1
(12 rows)

Time: 240.041 ms
  • I think we can move those to a new cg.identifier.project if we create one
  • The cg.identifier.cpwfproject field is similarly sparse, but the CCAFS ones are widely used