CGSpace Notes

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

September, 2022

in  Notes

2022-09-01

  • A bit of work on the “Mapping CG Core–CGSpace–MEL–MARLO Types” spreadsheet
  • I tested an item submission on DSpace Test with the Cocoon org.apache.cocoon.uploads.autosave=false change
    • The submission works as expected
  • Start debugging some region-related issues with csv-metadata-quality
    • I created a new test file test-geography.csv with some different scenarios
    • I also fixed a few bugs and improved the region-matching logic

2022-09-02

  • I worked a bit more on exclusion and skipping logic in csv-metadata-quality
    • I also pruned and updated all the Python dependencies
    • Then I released version 0.6.0 now that the excludes and region matching support is working way better

2022-09-05

  • Started a harvest on AReS last night
  • Looking over the Solr statistics from last month I see many user agents that look suspicious:
    • Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.2; WOW64; Trident/7.0; .NET4.0E; .NET4.0C)
    • Mozilla / 5.0(Windows NT 10.0; Win64; x64) AppleWebKit / 537.36(KHTML, like Gecko) Chrome / 77.0.3865.90 Safari / 537.36
    • Mozilla/5.0 (Windows NT 10.0; WOW64; Rv:50.0) Gecko/20100101 Firefox/50.0
    • Mozilla/5.0 (X11; Linux i686; rv:2.0b12pre) Gecko/20110204 Firefox/4.0b12pre
    • Mozilla/5.0 (Windows NT 10.0; Win64; x64; Xbox; Xbox One) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/103.0.0.0 Safari/537.36 Edge/44.18363.8131
    • Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1; SV1)
    • Mozilla/4.0 (compatible; MSIE 4.5; Windows 98;)
    • curb
    • bitdiscovery
    • omgili/0.5 +http://omgili.com
    • Mozilla/5.0 (compatible)
    • Vizzit
    • Mozilla/5.0 (Windows NT 5.1; rv:52.0) Gecko/20100101 Firefox/52.0
    • Mozilla/5.0 (Android; Mobile; rv:13.0) Gecko/13.0 Firefox/13.0
    • Java/17-ea
    • AdobeUxTechC4-Async/3.0.12 (win32)
    • ZaloPC-win32-24v473
    • Mozilla/5.0/Firefox/42.0 - nbertaupete95(at)gmail.com
    • Scoop.it
    • Mozilla/5.0 (Windows NT 6.1; rv:27.0) Gecko/20100101 Firefox/27.0
    • Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)
    • ows NT 10.0; WOW64; rv: 50.0) Gecko/20100101 Firefox/50.0
    • WebAPIClient
    • Mozilla/5.0 Firefox/26.0
    • Mozilla/5.0 (compatible; woorankreview/2.0; +https://www.woorank.com/)
  • For example, some are apparently using versions of Firefox that are over ten years old, and some are obviously trying to look like valid user agents, but making typos (Mozilla / 5.0)
  • Tons of hosts making requests likt this:
GET /bitstream/handle/10568/109408/Milk%20testing%20lab%20protocol.pdf?sequence=1&isAllowed=\x22><script%20>alert(String.fromCharCode(88,83,83))</script> HTTP/1.1" 400 5 "-" "Mozilla/5.0 (Windows NT 10.0; WOW64; Rv:50.0) Gecko/20100101 Firefox/50.0
  • I got a list of hosts making requests like that so I can purge their hits:
# zcat /var/log/nginx/{access,library-access,oai,rest}.log.[123]*.gz | grep 'String.fromCharCode(' | awk '{print $1}' | sort -u > /tmp/ips.txt 

$ awk '{print $1}' /tmp/hetzner.txt | wc -l
36
$ sort -u /tmp/hetzner-combined.txt  | wc -l
49
  • I will add this new list to nginx’s bot-networks.conf so they get throttled on scraping XMLUI and get classified as bots in Solr statistics
  • Then I purged hits from the following user agents:
$ ./ilri/check-spider-hits.sh -f /tmp/agents
Found 374 hits from curb in statistics
Found 350 hits from bitdiscovery in statistics
Found 564 hits from omgili in statistics
Found 390 hits from Vizzit in statistics
Found 9125 hits from AdobeUxTechC4-Async in statistics
Found 97 hits from ZaloPC-win32-24v473 in statistics
Found 518 hits from nbertaupete95 in statistics
Found 218 hits from Scoop.it in statistics
Found 584 hits from WebAPIClient in statistics

Total number of hits from bots: 12220
  • Then I will add these user agents to the ILRI spider override in DSpace

2022-09-06

  • I’m testing dspace-statistics-api with our DSpace 7 test server
    • After setting up the env and the database the python -m dspace_statistics_api.indexer runs without issues
    • While playing with Solr I tried to search for statistics from this month using time:2022-09* but I get this error: “Can’t run prefix queries on numeric fields”
    • I guess that the syntax in Solr changed since 4.10…
    • This works, but is super annoying: time:[2022-09-01T00:00:00Z TO 2022-09-30T23:59:59Z]

2022-09-07

  • I tested the controlled-vocabulary changes on DSpace 6 and they work fine
    • Last week I found that DSpace 7 is more strict with controlled vocabularies and requires IDs for all node values
    • This is a pain because it means I have to re-do the IDs in each file every time I update them
    • If I add id="0000" to each, then I can use this vim expression let i=0001 | g/0000/s//\=i/ | let i=i+1 to replace the numbers with increments starting from 1
  • Meeting with Marie Angelique, Abenet, Sarа, аnd Margarita to continue the discussion about Types from last week
    • We made progress with concrete actions and will continue next week

2022-09-08

  • I had a meeting with Nicky from UNEP to discuss issues they are having with their DSpace
    • I told her about the meeting of DSpace community people that we’re planning at ILRI in the next few weeks

2022-09-09

  • Add some value mappings to AReS because I see a lot of incorrect regions and countries
  • I also found some values that were blank in CGSpace so I deleted them:
dspace=# BEGIN;
BEGIN
dspace=# DELETE FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value='';
DELETE 70
dspace=# COMMIT;
COMMIT
  • Start a full Discovery index on CGSpace to catch these changes in the Discovery

2022-09-11

  • Today is Sunday and I see the load on the server is high
    • Google and a bunch of other bots have been blocked on XMLUI for the past two weeks so it’s not from them!
    • Looking at the top IPs this morning:
# cat /var/log/nginx/{access,library-access,oai,rest}.log /var/log/nginx/{access,library-access,oai,rest}.log.1 | grep '11/Sep/2022' | awk '{print $1}' | sort | uniq -c | sort -h | tail -n 40
...
    165 64.233.172.79
    166 87.250.224.34
    200 69.162.124.231
    202 216.244.66.198
    385 207.46.13.149
    398 207.46.13.147
    421 66.249.64.185
    422 157.55.39.81
    442 2a01:4f8:1c17:5550::1
    451 64.124.8.36
    578 137.184.159.211
    597 136.243.228.195
   1185 66.249.64.183
   1201 157.55.39.80
   3135 80.248.237.167
   4794 54.195.118.125
   5486 45.5.186.2
   6322 2a01:7e00::f03c:91ff:fe9a:3a37
   9556 66.249.64.181
  • The top is still Google, but all the requests are HTTP 503 because I classified them as bots for XMLUI at least
  • Then there’s 80.248.237.167, which is using a normal user agent and scraping Discovery
    • That IP is on Internet Vikings aka Internetbolaget and we are already marking that subnet as ‘bot’ for XMLUI so most of these requests are HTTP 503
  • On another note, I’m curious to explore enabling caching of certain REST API responses
    • For example, where the use is for harvesting rather than actual clients getting bitstreams or thumbnails, it seems there might be a benefit to speeding these up for subsequent requestors:
# awk '{print $7}' /var/log/nginx/rest.log | grep -v retrieve | sort | uniq -c | sort -h | tail -n 10
      4 /rest/items/3f692ddd-7856-4bf0-a587-99fb3df0688a/bitstreams
      4 /rest/items/3f692ddd-7856-4bf0-a587-99fb3df0688a/metadata
      4 /rest/items/b014e36f-b496-43d8-9148-cc9db8a6efac/bitstreams
      4 /rest/items/b014e36f-b496-43d8-9148-cc9db8a6efac/metadata
      5 /rest/handle/10568/110310?expand=all
      5 /rest/handle/10568/89980?expand=all
      5 /rest/handle/10568/97614?expand=all
      6 /rest/handle/10568/107086?expand=all
      6 /rest/handle/10568/108503?expand=all
      6 /rest/handle/10568/98424?expand=all
  • I specifically have to not cache things like requests for bitstreams because those are from actual users and we need to keep the real requests so we get the statistics hit
    • Will be interesting to check the results above as the day goes on (now 10AM)
    • To estimate the potential savings from caching I will check how many non-bitstream requests are made versus how many are made more than once (updated the next morning using yesterday’s log):
# awk '{print $7}' /var/log/nginx/rest.log.1 | grep -v retrieve | sort -u | wc -l
33733
# awk '{print $7}' /var/log/nginx/rest.log.1 | grep -v retrieve | sort | uniq -c | awk '$1 > 1' | wc -l
5637
  • In the afternoon I started a harvest on AReS (which should affect the numbers above also)
  • I enabled an nginx proxy cache on DSpace Test for this location regex: location ~ /rest/(handle|items|collections|communities)/.+

2022-09-12

  • I am testing harvesting DSpace Test via AReS with the nginx proxy cache enabled
    • I had to tune the regular expression in nginx a bit because the REST requests OpenRXV uses weren’t matching
    • Now I’m trying this one: /rest/(handle|items|collections|communities)/?
    • Testing in regex101.com with this test string:
/rest/handle/10568/27611
/rest/items?expand=metadata,parentCommunityList,parentCollectionList,bitstreams&limit=10&offset=36270
/rest/handle/10568/110310?expand=all
/rest/rest/bitstreams/28926633-c7c2-49c2-afa8-6d81cadc2316/retrieve
/rest/bitstreams/15412/retrieve
/rest/items/083dbb0d-11e2-4dfe-902b-eb48e4640d04/metadata
/rest/items/083dbb0d-11e2-4dfe-902b-eb48e4640d04/bitstreams
/rest/collections/edea23c0-0ebd-4525-90b0-0b401f997704/items
/rest/items/14507941-aff2-4d57-90bd-03a0733ad859/metadata
/rest/communities/b38ea726-475f-4247-a961-0d0b76e67f85/collections
/rest/collections/e994c450-6ff7-41c6-98df-51e5c424049e/items?limit=10000
  • I estimate that it will take about 1GB of cache to harvest 100,000 items from CGSpace with OpenRXV (10,000 pages)
  • Basically all but 4 and 5 (bitstreams) should match
  • Upload 682 OICRs from MARLO to CGSpace
    • We had tested these on DSpace Test last month along with the MELIAs, Policies, and Innovations, but we decided to upload the OICRs first so that other things can link against them as related items

2022-09-14

  • Meeting with Peter, Abenet, Indira, and Michael about CGSpace rollout plan for the Initiatives

2022-09-16

  • Meeting with Marie-Angeqlique, Abenet, Margarita, and Sara about types for CG Core
    • We are about halfway through the list of types now, with concrete actions for CG Core and CGSpace
    • We will meet next in two weeks to hopefully finalize the list, then we can move on to definitions

2022-09-18

  • Deploy the org.apache.cocoon.uploads.autosave=false change on CGSpace
  • Start a harvest on AReS

2022-09-19

  • Deploy the nginx proxy cache for /rest requests on CGSpace
    • I had tested this last week on DSpace Test
    • By my counts on CGSpace yesterday (Sunday, a busy day for the REST API), we had 5,654 URLs that were requested more than twice, and it tails off after that towards two, three, four, etc:
# awk '{print $7}' /var/log/nginx/rest.log.1 | grep -v retrieve | sort | uniq -c | awk '$1 > 1' | wc -l
5654
# awk '{print $7}' /var/log/nginx/rest.log.1 | grep -v retrieve | sort | uniq -c | awk '$1 == 2' | wc -l
4710
# awk '{print $7}' /var/log/nginx/rest.log.1 | grep -v retrieve | sort | uniq -c | awk '$1 == 3' | wc -l
814
# awk '{print $7}' /var/log/nginx/rest.log.1 | grep -v retrieve | sort | uniq -c | awk '$1 == 4' | wc -l
86
# awk '{print $7}' /var/log/nginx/rest.log.1 | grep -v retrieve | sort | uniq -c | awk '$1 == 5' | wc -l
39
  • For now I guess requests that were done two or three times by different clients will be cached and that’s a win, and I expect more and more REST API activity soon when initiatives and One CGIAR stuff picks up

2022-09-20

  • I checked the status of the nginx REST API cache on CGSpace and it was stuck at 7,083 items for hours:
# find /var/cache/nginx/rest_cache/ -type f | wc -l
7083
  • The proxy cache key zone is currently 1m, which can store ~8,000 keys, so that could be what we’re running into
    • I increased it to 2m and will keep monitoring it
  • CIP webmaster contacted me to say they are having problems harvesting CGSpace from their WordPress
    • I am not sure if there are issues due to the REST API caching I enabled…

2022-09-21

  • Planning the Nairobi DSpace Users meeting with Abenet
  • Planning to have a call about MEL submitting to CGSpace on Monday with Mohammed Salem
    • I created two collections on DSpace Test: one with a workflow, and one without
    • According to my notes from 2020-10 the account must be in the admin group in order to submit via the REST API, so I added it to the admin group of each collection

2022-09-22

  • Nairobi DSpace users meeting at ILRI
  • I found a few users that didn’t have ORCID iDs and were missing tags on CGSpace so I tagged them:
dc.contributor.author,cg.creator.identifier
dc.contributor.author,cg.creator.identifier
"Alonso, Silvia","Silvia Alonso: 0000-0002-0565-536X"
"Goopy, John P.","John Goopy: 0000-0001-7177-1310"
"Korir, Daniel","Daniel Korir: 0000-0002-1356-8039"
"Leitner, Sonja","Sonja Leitner: 0000-0002-1276-8071"
"Fèvre, Eric M.","Eric M. Fèvre: 0000-0001-8931-4986"
"Galiè, Alessandra","Alessandra Galie: 0000-0001-9868-7733"
"Baltenweck, Isabelle","Isabelle Baltenweck: 0000-0002-4147-5921"
"Robinson, Timothy P.","Timothy Robinson: 0000-0002-4266-963X"
"Lannerstad, Mats","Mats Lannerstad: 0000-0002-5116-3198"
"Graham, Michael","Michael Graham: 0000-0002-1189-8640"
"Merbold, Lutz","Lutz Merbold: 0000-0003-4974-170X"
"Rufino, Mariana C.","Mariana Rufino: 0000-0003-4293-3290"
"Wilkes, Andreas","Andreas Wilkes: 0000-0001-7546-991X"
"van der Weerden, T.","Tony van der Weerden: 0000-0002-6999-2584"
"Vermeulen, S.","Sonja Vermeulen: 0000-0001-6242-9513"
"Vermeulen, Sonja","Sonja Vermeulen: 0000-0001-6242-9513"
"Vermeulen, Sonja J.","Sonja Vermeulen: 0000-0001-6242-9513"
"Hung Nguyen-Viet","Hung Nguyen-Viet: 0000-0003-1549-2733"
"Herrero, Mario T.","Mario Herrero: 0000-0002-7741-5090"
"Thornton, Philip K.","Philip Thornton: 0000-0002-1854-0182"
"Duncan, Alan J.","Alan Duncan: 0000-0002-3954-3067"
"Lukuyu, Ben A.","Ben Lukuyu: 0000-0002-9374-3553"
"Lindahl, Johanna F.","Johanna Lindahl: 0000-0002-1175-0398"
"Okeyo Mwai, Ally","Ally Okeyo Mwai: 0000-0003-2379-7801"
"Wieland, Barbara","Barbara Wieland: 0000-0003-4020-9186"
"Omore, Amos O.","Amos Omore: 0000-0001-9213-9891"
"Randolph, Thomas F.","Thomas Fitz Randolph: 0000-0003-1849-9877"
"Staal, Steven J.","Steven Staal: 0000-0002-1244-1773"
"Hanotte, Olivier H.","Olivier Hanotte: 0000-0002-2877-4767"
"Dessie, Tadelle","Tadelle Dessie: 0000-0002-1630-0417"
"Dione, Michel M.","Michel Dione: 0000-0001-7812-5776"
"Gebremedhin, Berhanu","Berhanu Gebremedhin: 0000-0002-3168-2783"
"Ouma, Emily A.","Emily Ouma: 0000-0002-3123-1376"
"Roesel, Kristina","Kristina Roesel: 0000-0002-2553-1129"
"Bishop, Richard P.","Richard Bishop: 0000-0002-3720-9970"
"Lapar, Ma. Lucila","Ma. Lucila Lapar: 0000-0002-4214-9845"
"Rich, Karl M.","Karl Rich: 0000-0002-5581-9553"
"Hoekstra, Dirk","Dirk Hoekstra: 0000-0002-6111-6627"
"Nene, Vishvanath","Vishvanath Nene: 0000-0001-7066-4169"
"Patel, S.P.","Sonal Henson: 0000-0002-2002-5462"
"Hanson, Jean","Jean Hanson: 0000-0002-3648-2641"
"Marshall, Karen","Karen Marshall: 0000-0003-4197-1455"
"Notenbaert, An Maria Omer","An Maria Omer Notenbaert: 0000-0002-6266-2240"
"Ojango, Julie M.K.","Ojango J.M.K.: 0000-0003-0224-5370"
"Wijk, Mark T. van","Mark van Wijk: 0000-0003-0728-8839"
"Tarawali, Shirley A.","Shirley Tarawali: 0000-0001-9398-8780"
"Naessens, Jan","Jan Naessens: 0000-0002-7075-9915"
"Butterbach-Bahl, Klaus","Klaus Butterbach-Bahl: 0000-0001-9499-6598"
"Poole, Elizabeth J.","Elizabeth Jane Poole: 0000-0002-8570-794X"
"Mulema, Annet A.","Annet Mulema: 0000-0003-4192-3939"
"Dror, Iddo","Iddo Dror: 0000-0002-0800-7456"
"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
"Baker, Derek","Derek Baker: 0000-0001-6020-6973"
"Ericksen, Polly J.","Polly Ericksen: 0000-0002-5775-7691"
"Jones, Christopher S.","Chris Jones: 0000-0001-9096-9728"
"Mude, Andrew G.","Andrew Mude: 0000-0003-4903-6613"
"Puskur, Ranjitha","Ranjitha Puskur: 0000-0002-9112-3414"
"Kiara, Henry K.","Henry Kiara: 0000-0001-9578-1636"
"Gibson, John P.","John Gibson: 0000-0003-0371-2401"
"Flintan, Fiona E.","Fiona Flintan: 0000-0002-9732-097X"
"Mrode, Raphael A.","Raphael Mrode: 0000-0003-1964-5653"
"Mtimet, Nadhem","Nadhem Mtimet: 0000-0003-3125-2828"
"Said, Mohammed Yahya","Mohammed Yahya Said: 0000-0001-8127-6399"
"Pezo, Danilo A.","Danilo Pezo: 0000-0001-5345-5314"
"Haileslassie, Amare","Amare Haileslassie: 0000-0001-5237-9006"
"Wright, Iain A.","Iain Wright: 0000-0002-6216-5308"
"Cadilhon, Joseph J.","Jean-Joseph Cadilhon: 0000-0002-3181-5136"
"Domelevo Entfellner, Jean-Baka","Jean-Baka Domelevo Entfellner: 0000-0002-8282-1325"
"Oyola, Samuel O.","Samuel O. Oyola: 0000-0002-6425-7345"
"Agaba, M.","Morris Agaba: 0000-0001-6777-0382"
"Beebe, Stephen E.","Stephen E Beebe: 0000-0002-3742-9930"
"Ouso, Daniel","Daniel Ouso: 0000-0003-0994-2558"
"Ouso, Daniel O.","Daniel Ouso: 0000-0003-0994-2558"
"Rono, Gilbert K.","Gilbert Kibet-Rono: 0000-0001-8043-5423"
"Kibet, Gilbert","Gilbert Kibet-Rono: 0000-0001-8043-5423"
"Juma, John","John Juma: 0000-0002-1481-5337"
"Juma, J.","John Juma: 0000-0002-1481-5337"
$ ./ilri/add-orcid-identifiers-csv.py -i /tmp/2022-09-22-add-orcids.csv -db dspace -u dspace -p 'fuuu'
  • This adds nearly 5,500 ORCID tags!
    • Some of these authors were not in the controlled vocabulary so I added them

2022-09-23

  • Tag some more ORCID metdata (amended above)
  • Meeting with Peter and Abenet to discuss CGSpace issues
    • We found a workable solution to the MEL submission issue: they can submit to a dedicated MEL-only collection with no workflow and we will map or move the items after
  • Pascal says that they have made a pull request for their duplicate checker on DSpace 7 yayyyy

2022-09-24

  • Found some more ORCID identifiers to tag so I added them to the list above
  • Start a harvest on AReS around 8PM on Saturday night

2022-09-25

  • The harvest on AReS finished and now the load on CGSpace server is still high like always on Sunday mornings
    • UptimeRobot says it’s down sigh…
  • I had an idea to include the HTTP Accept header in the nginx proxy cache key to fix the issue we had with CIP last week
    • It seems to work:
$ http --print Hh 'https://dspacetest.cgiar.org/rest/items?expand=metadata,parentCommunityList,parentCollectionList,bitstreams&limit=10&offset=60'
...
Content-Type: application/json
X-Cache-Status: MISS

$ http --print Hh 'https://dspacetest.cgiar.org/rest/items?expand=metadata,parentCommunityList,parentCollectionList,bitstreams&limit=10&offset=60'
...
Content-Type: application/json
X-Cache-Status: HIT

$ http --print Hh 'https://dspacetest.cgiar.org/rest/items?expand=metadata,parentCommunityList,parentCollectionList,bitstreams&limit=10&offset=60' Accept:application/xml
...
Content-Type: application/xml
X-Cache-Status: MISS

$ http --print Hh 'https://dspacetest.cgiar.org/rest/items?expand=metadata,parentCommunityList,parentCollectionList,bitstreams&limit=10&offset=60' Accept:application/xml
...
Content-Type: application/xml
X-Cache-Status: HIT
  • This effectively makes our cache half as effective, but hopefully as more people start harvesting the number of requests handled by it will go up
  • I will enable this on CGSpace and email Moises from CIP to check if their harvester is working

2022-09-26

  • Update welcome text on CGSpace after our meeting last week
  • I found another dozen or so ORCIDs for top authors on ILRI’s community on CGSpace and tagged them (~1,100 more metadata fields)
  • Last week we discussed moving cg.identifier.googleurl to cg.identifier.url since there is no need to treat Google Books URLs specially anymore as far as we know
    • I made the changes to the submission form and the XMLUI item displays, then moved all existing metadata in PostgreSQL:
dspace= ☘ UPDATE metadatavalue SET metadata_field_id=219 WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=222;
UPDATE 1137
  • Then I deleted cg.identifier.googleurl from the metadata registry
  • Meeting with Salem, Svetlana, Valentina, and Abenet about MEL depositing to CGSpace for the initiatives
    • Submitting to a collection without a workflow works as expected, and we can even select another collection (with a workflow) to map the item to from the MEL submission
    • The three minor issues we found were:
      • MEL still doesn’t send the bitstream
      • MEL sends metadata with a download URL on mel.cgiar.org
      • MEL sends a JPEG that says “no thumbnail” when an item doesn’t have a thumbnail
    • I still need to send feedback to the group