CGSpace Notes

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

July, 2022

in  Notes

2022-07-02

  • I learned how to use the Levenshtein functions in PostgreSQL
    • The thing is that there is a limit of 255 characters for these functions in PostgreSQL so you need to truncate the strings before comparing
    • Also, the trgm functions I’ve used before are case insensitive, but Levenshtein is not, so you need to make sure to lower case both strings first
  • A working query checking for duplicates in the recent AfricaRice items is:
localhost/dspace= ☘ SELECT text_value FROM metadatavalue WHERE  dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=64 AND levenshtein_less_equal(LOWER('International Trade and Exotic Pests: The Risks for Biodiversity and African Economies'), LEFT(LOWER(text_value), 255), 3) <= 3;
                                       text_value                                       
────────────────────────────────────────────────────────────────────────────────────────
 International trade and exotic pests: the risks for biodiversity and African economies
(1 row)

Time: 399.751 ms

2022-07-03

  • Start a harvest on AReS

2022-07-04

  • Linode told me that CGSpace had high load yesterday
    • I also got some up and down notices from UptimeRobot
    • Looking now, I see there was a very high CPU and database pool load, but a mostly normal DSpace session count

CPU load day JDBC pool day

  • Seems we have some old database transactions since 2022-06-27:

PostgreSQL locks week PostgreSQL query length week

  • Looking at the top connections to nginx yesterday:
# awk '{print $1}' /var/log/nginx/{access,library-access,oai,rest}.log.1 | sort | uniq -c | sort -h | tail
   1132 64.124.8.34
   1146 2a01:4f8:1c17:5550::1
   1380 137.184.159.211
   1533 64.124.8.59
   4013 80.248.237.167
   4776 54.195.118.125
  10482 45.5.186.2
  11177 172.104.229.92
  15855 2a01:7e00::f03c:91ff:fe9a:3a37
  22179 64.39.98.251
  • And the total number of unique IPs:
# awk '{print $1}' /var/log/nginx/{access,library-access,oai,rest}.log.1 | sort -u | wc -l
6952
  • This seems low, so it must have been from the request patterns by certain visitors
    • 64.39.98.251 is Qualys, and I’m debating blocking all their IPs using a geo block in nginx (need to test)
    • The top few are known ILRI and other CGIAR scrapers, but 80.248.237.167 is on InternetVikings in Sweden, using a normal user agentand scraping Discover
    • 64.124.8.59 is making requests with a normal user agent and belongs to Castle Global or Zayo
  • I ran all system updates and rebooted the server (could have just restarted PostgreSQL but I thought I might as well do everything)
  • I implemented a geo mapping for the user agent mapping AND the nginx limit_req_zone by extracting the networks into an external file and including it in two different geo mapping blocks
    • This is clever and relies on the fact that we can use defaults in both cases
    • First, we map the user agent of requests from these networks to “bot” so that Tomcat and Solr handle them accordingly
    • Second, we use this as a key in a limit_req_zone, which relies on a default mapping of ’’ (and nginx doesn’t evaluate empty cache keys)
  • I noticed that CIP uploaded a number of Georgian presentations with dcterms.language set to English and Other so I changed them to “ka”
    • Perhaps we need to update our list of languages to include all instead of the most common ones
  • I wrote a script ilri/iso-639-value-pairs.py to extract the names and Alpha 2 codes for all ISO 639-1 languages from pycountry and added them to input-forms.xml

2022-07-06

  • CGSpace went down and up a few times due to high load
    • I found one host in Romania making very high speed requests with a normal user agent (Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.2; WOW64; Trident/7.0; .NET4.0E; .NET4.0C):
# awk '{print $1}' /var/log/nginx/{access,library-access,oai,rest}.log | sort | uniq -c | sort -h | tail -n 10
    516 142.132.248.90
    525 157.55.39.234
    587 66.249.66.21
    593 95.108.213.59
   1372 137.184.159.211
   4776 54.195.118.125
   5441 205.186.128.185
   6267 45.5.186.2
  15839 2a01:7e00::f03c:91ff:fe9a:3a37
  36114 146.19.75.141
  • I added 146.19.75.141 to the list of bot networks in nginx
  • While looking at the logs I started thinking about Bing again
  • Delete two items on CGSpace for Margarita because she was getting the “Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:0b26875a-…” error
    • This is the same DSpace 6 bug I noticed in 2021-03, 2021-04, and 2021-05
  • Update some cg.audience metadata to use “Academics” instead of “Academicians”:
dspace=# UPDATE metadatavalue SET text_value='Academics' WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=144 AND text_value='Academicians';
UPDATE 104
  • I will also have to remove “Academicians” from input-forms.xml

2022-07-07

  • Finalize lists of non-AGROVOC subjects in CGSpace that I started last week 
localhost/dspace= ☘ SELECT DISTINCT(ds6_item2collectionhandle(dspace_object_id)) AS collection, COUNT(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND LOWER(text_value) = 'water demand' GROUP BY collection ORDER BY count DESC LIMIT 5;
 collection  │ count 
─────────────┼───────
 10568/36178 │    56
 10568/36185 │    46
 10568/36181 │    35
 10568/36188 │    28
 10568/36179 │    21
(5 rows)
  • For now I only did terms from my list that had 100 or more occurrences in CGSpace
    • This leaves us with thirty-six terms that I will send to Sara Jani and Elizabeth Arnaud for evaluating possible inclusion to AGROVOC
  • Write to some submitters from CIAT, Bioversity, and CCAFS to ask if they are still uploading new items with their legacy subject fields on CGSpace
    • We want to remove them from the submission form to create space for new fields
  • Update one term I noticed people using that was close to AGROVOC:
dspace=# UPDATE metadatavalue SET text_value='development policies' WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=187 AND text_value='development policy';
UPDATE 108
  • After contacting some editors I removed some old metadata fields from the submission form and browse indexes:
    • Bioversity subject (cg.subject.bioversity)
    • CCAFS phase 1 project tag (cg.identifier.ccafsproject)
    • CIAT project tag (cg.identifier.ciatproject)
    • CIAT subject (cg.subject.ciat)
  • Work on cleaning and proofing forty-six AfricaRice items for CGSpace
    • Last week we identified some duplicates so I removed those
    • The data is of mediocre quality
    • I’ve been fixing citations (nitpick), adding licenses, adding volume/issue/extent, fixing DOIs, and adding some AGROVOC subjects
    • I even found titles that have typos, looking something like OCR errors…

2022-07-08

  • Finalize the cleaning and proofing of AfricaRice records
    • I found two suspicious items that claim to have been published but I can’t find in the respective journals, so I removed those
    • I uploaded the forty-four items to DSpace Test
  • Margarita from CCAFS said they are no longer using the CCAFS subject or CCAFS phase 2 project tag
    • I removed these from the input-form.xml and Discovery facets:
      • cg.identifier.ccafsprojectpii
      • cg.subject.cifor
    • For now we will keep them in the search filters
  • I modified my check-duplicates.py script a bit to fix a logic error for deleted items and add similarity scores from spacy (see: https://stackoverflow.com/questions/8897593/how-to-compute-the-similarity-between-two-text-documents)
    • I want to use this with the MARLO innovation reports, to find related publications and working papers on CGSpace
    • I am curious to see how the similarity scores compare to those from trgm… perhaps we don’t need them actually
  • Deploy latest changes to submission form, Discovery, and browse on CGSpace
    • Also run all system updates and reboot the host
  • Fix 152 dcterms.relation that are using “cgspace.cgiar.org” links instead of handles:
UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, '.*cgspace\.cgiar\.org/handle/(\d+/\d+)$', 'https://hdl.handle.net/\1') WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=180 AND text_value ~ 'cgspace\.cgiar\.org/handle/\d+/\d+$';

2022-07-10

  • UptimeRobot says that CGSpace is down
    • I see high load around 22, high CPU around 800%
    • Doesn’t seem to be a lot of unique IPs:
# awk '{print $1}' /var/log/nginx/{access,library-access,oai,rest}.log | sort -u | wc -l
2243

Looking at the top twenty I see some usual IPs, but some new ones on Hetzner that are using many DSpace sessions:

$ grep 65.109.2.97 dspace.log.2022-07-10 | grep -oE 'session_id=[A-Z0-9]{32}:ip_addr=' | sort | uniq | wc -l
1613
$ grep 95.216.174.97 dspace.log.2022-07-10 | grep -oE 'session_id=[A-Z0-9]{32}:ip_addr=' | sort | uniq | wc -l
1696
$ grep 65.109.15.213 dspace.log.2022-07-10 | grep -oE 'session_id=[A-Z0-9]{32}:ip_addr=' | sort | uniq | wc -l
1708
$ grep 65.108.80.78 dspace.log.2022-07-10 | grep -oE 'session_id=[A-Z0-9]{32}:ip_addr=' | sort | uniq | wc -l
1830
$ grep 65.108.95.23 dspace.log.2022-07-10 | grep -oE 'session_id=[A-Z0-9]{32}:ip_addr=' | sort | uniq | wc -l
1811

DSpace sessions week

  • These IPs are using normal-looking user agents:

    • Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:52.9) Gecko/20100101 Goanna/4.1 Firefox/52.9 PaleMoon/28.0.0.1
    • Mozilla/5.0 (Windows NT 10.0; WOW64; rv:40.0) Gecko/20100101 Firefox/45.0"
    • Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:56.0) Gecko/20100101 Firefox/56.0.1 Waterfox/56.0.1
    • Mozilla/5.0 (Windows NT 10.0; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/71.0.3578.85 Safari/537.36

  • I will add networks I’m seeing now to nginx’s bot-networks.conf for now (not all of Hetzner) and purge the hits later:

    • 65.108.0.0/16
    • 65.21.0.0/16
    • 95.216.0.0/16
    • 135.181.0.0/16
    • 138.201.0.0/16

  • I think I’m going to get to a point where I categorize all commercial subnets as bots by default and then whitelist those we need

  • Sheesh, there are a bunch more IPv6 addresses also on Hetzner:

# awk '{print $1}' /var/log/nginx/{access,library-access}.log | sort | grep 2a01:4f9 | uniq -c | sort -h
      1 2a01:4f9:6a:1c2b::2
      2 2a01:4f9:2b:5a8::2
      2 2a01:4f9:4b:4495::2
     96 2a01:4f9:c010:518c::1
    137 2a01:4f9:c010:a9bc::1
    142 2a01:4f9:c010:58c9::1
    142 2a01:4f9:c010:58ea::1
    144 2a01:4f9:c010:58eb::1
    145 2a01:4f9:c010:6ff8::1
    148 2a01:4f9:c010:5190::1
    149 2a01:4f9:c010:7d6d::1
    153 2a01:4f9:c010:5226::1
    156 2a01:4f9:c010:7f74::1
    160 2a01:4f9:c010:5188::1
    161 2a01:4f9:c010:58e5::1
    168 2a01:4f9:c010:58ed::1
    170 2a01:4f9:c010:548e::1
    170 2a01:4f9:c010:8c97::1
    175 2a01:4f9:c010:58c8::1
    175 2a01:4f9:c010:aada::1
    182 2a01:4f9:c010:58ec::1
    182 2a01:4f9:c010:ae8c::1
    502 2a01:4f9:c010:ee57::1
    530 2a01:4f9:c011:567a::1
    535 2a01:4f9:c010:d04e::1
    539 2a01:4f9:c010:3d9a::1
    586 2a01:4f9:c010:93db::1
    593 2a01:4f9:c010:a04a::1
    601 2a01:4f9:c011:4166::1
    607 2a01:4f9:c010:9881::1
    640 2a01:4f9:c010:87fb::1
    648 2a01:4f9:c010:e680::1
   1141 2a01:4f9:3a:2696::2
   1146 2a01:4f9:3a:2555::2
   3207 2a01:4f9:3a:2c19::2
  • Maybe it’s time I ban all of Hetzner… sheesh.
  • I left for a few hours and the server was going up and down the whole time, still very high CPU and database when I got back

CPU day

  • I am not sure what’s going on
    • I extracted all the IPs and used resolve-addresses-geoip2.py to analyze them and extract all the Hetzner networks and block them
    • It’s 181 IPs on Hetzner…
  • I rebooted the server to see if it was just some stuck locks in PostgreSQL…
  • The load is still higher than I would expect, and after a few more hours I see more Hetzner IPs coming through? Two more subnets to block
  • Start a harvest on AReS

2022-07-12

  • Update an incorrect ORCID identifier for Alliance
  • Adjust collection permissions on CIFOR publications collection so Vika can submit without approval

2022-07-14

  • Someone on the DSpace Slack mentioned having issues with the database configuration in DSpace 7.3
    • The reason is apparently that the default db.dialect changed from “org.dspace.storage.rdbms.hibernate.postgres.DSpacePostgreSQL82Dialect” to “org.hibernate.dialect.PostgreSQL94Dialect” as a result of a Hibernate update
  • Then I was getting more errors starting the backend server in Tomcat, but the issue was that the backend server needs Solr to be up first!

2022-07-17

  • Start a harvest on AReS around 3:30PM
  • Later in the evening I see CGSpace was going down and up (not as bad as last Sunday) with around 18.0 load…
  • I see very high CPU usage:

CPU day

  • But DSpace sessions are normal (not like last weekend):

DSpace sessions week

  • I see some Hetzner IPs in the top users today, but most of the requests are getting HTTP 503 because of the changes I made last week
  • I see 137.184.159.211, which is on Digital Ocean, and the DNS is apparently iitawpsite.iita.org
    • I’ve seen their user agent before, but I don’t think I knew it was IITA: “GuzzleHttp/6.3.3 curl/7.84.0 PHP/7.4.30”
    • I already have something in nginx to mark Guzzle as a bot, but interestingly it shows up in Solr as $http_user_agent so there is a logic error in my nginx config
  • Ouch, the logic error seems to be this:
geo $ua {
    default          $http_user_agent;

    include /etc/nginx/bot-networks.conf;
}
  • After some testing on DSpace Test I see that this is actually setting the default user agent to a literal $http_user_agent
  • The nginx map docs say:

The resulting value can contain text, variable (0.9.0), and their combination (1.11.0).

  • But I can’t get it to work, neither for the default value or for matching my IP…
    • I will have to ask on the nginx mailing list
  • The total number of requests and unique hosts was not even very high (below here around midnight so is almost all day):
# awk '{print $1}' /var/log/nginx/{access,library-access,oai,rest}.log | sort -u | wc -l
2776
# awk '{print $1}' /var/log/nginx/{access,library-access,oai,rest}.log | wc -l
40325

2022-07-18

  • Reading more about nginx’s geo/map and doing some tests on DSpace Test, it appears that the geo module cannot do dynamic values
    • So this issue with the literal $http_user_agent is due to the geo block I put in place earlier this month
    • I reworked the logic so that the geo block sets “bot” or and empty string when a network matches or not, and then re-use that value in a mapping that passes through the host’s user agent in case geo has set it to an empty string
    • This allows me to accomplish the original goal while still only using one bot-networks.conf file for the limit_req_zone and the user agent mapping that we pass to Tomcat
    • Unfortunately this means I will have hundreds of thousands of requests in Solr with a literal $http_user_agent
    • I might try to purge some by enumerating all the networks in my block file and running them through check-spider-ip-hits.sh
  • I extracted all the IPs/subnets from bot-networks.conf and prepared them so I could enumerate their IPs
    • I had to add /32 to all single IPs, which I did with this crazy vim invocation:
:g!/\/\d\+$/s/^\(\d\+\.\d\+\.\d\+\.\d\+\)$/\1\/32/
  • Explanation:
    • g!: global, lines not matching (the opposite of g)
    • /\/\d\+$/, pattern matching / with one or more digits at the end of the line
    • s/^\(\d\+\.\d\+\.\d\+\.\d\+\)$/\1\/32/, for lines not matching above, capture the IPv4 address and add /32 at the end
  • Then I ran the list through prips to enumerate the IPs:
$ while read -r line; do prips "$line" | sed -e '1d; $d'; done < /tmp/bot-networks.conf > /tmp/bot-ips.txt
$ wc -l /tmp/bot-ips.txt                                                                                        
1946968 /tmp/bot-ips.txt
  • I started running check-spider-ip-hits.sh with the 1946968 IPs and left it running in dry run mode

2022-07-19

  • Patrizio and Fabio emailed me to ask if their IP was banned from CGSpace
    • It’s one of the Hetzner ones so I said yes definitely, and asked more about how they are using the API
  • Add ORCID identifer for Ram Dhulipala, Lilian Wambua, and Dan Masiga to CGSpace and tag them and some other existing items:
dc.contributor.author,cg.creator.identifier
"Dhulipala, Ram K","Ram Dhulipala: 0000-0002-9720-3247"
"Dhulipala, Ram","Ram Dhulipala: 0000-0002-9720-3247"
"Dhulipala, R.","Ram Dhulipala: 0000-0002-9720-3247"
"Wambua, Lillian","Lillian Wambua: 0000-0003-3632-7411"
"Wambua, Lilian","Lillian Wambua: 0000-0003-3632-7411"
"Masiga, D.K.","Daniel Masiga: 0000-0001-7513-0887"
"Masiga, Daniel K.","Daniel Masiga: 0000-0001-7513-0887"
"Jores, Joerg","Joerg Jores: 0000-0003-3790-5746"
"Schieck, Elise","Elise Schieck: 0000-0003-1756-6337"
"Schieck, Elise G.","Elise Schieck: 0000-0003-1756-6337"
$ ./ilri/add-orcid-identifiers-csv.py -i /tmp/2022-07-19-add-orcids.csv -db dspace -u dspace -p 'fuuu'
  • Review the AfricaRice records from earlier this month again
    • I found one more duplicate and one more suspicious item, so the total after removing those is now forty-two
  • I took all the ~560 IPs that had hits so far in check-spider-ip-hits.sh above (about 270,000 into the list of 1946968 above) and ran them directly on CGSpace
    • This purged 199,032 hits from Solr, very many of which were from Qualys, but also that Chinese bot on 124.17.34.0/24 that was grabbing PDFs a few years ago which I blocked in nginx, but never purged the hits from
    • Then I deleted all IPs up to the last one where I found hits in the large file of 1946968 IPs and re-started the script

2022-07-20

  • Did a few more minor edits to the forty-two AfricaRice records (including generating thumbnails for the handful that are Creative Commons licensed) then did a test import on my local instance
    • Once it worked well I did an import to CGSpace:
$ dspace import -a -e fuuu@example.com -m 2022-07-20-africarice.map -s /tmp/SimpleArchiveFormat
  • Also make edits to ~62 affiliations on CGSpace because I noticed they were messed up
  • Extract another ~1,600 IPs that had hits since I started the second round of check-spider-ip-hits.sh yesterday and purge another 303,594 hits
    • This is about 999846 into the original list of 1946968 from yesterday
    • A metric fuck ton of the IPs in this batch were from Hetzner

2022-07-21

  • Extract another ~2,100 IPs that had hits since I started the third round of check-spider-ip-hits.sh last night and purge another 763,843 hits
    • This is about 1441221 into the original list of 1946968 from two days ago
    • Again these are overwhelmingly Hetzner (not surprising since my bot-networks.conf file in nginx is mostly Hetzner)
  • I responded to my original request to Atmire about the log4j to reload4j migration in DSpace 6.4
    • I had initially requested a comment from them in 2022-05
  • Extract another ~1,200 IPs that had hits from the fourth round of check-spider-ip-hits.sh earlier today and purge another 74,591 hits
    • Now the list of IPs I enumerated from the nginx bot-networks.conf is finished

2022-07-22

  • I created a new Linode instance for testing DSpace 7
  • Jose from the CCAFS team sent me the final versions of 3,500+ Innovations, Policies, MELIAs, and OICRs from MARLO
  • I re-synced CGSpace with DSpace Test so I can have a newer snapshot of the production data there for testing the CCAFS MELIAs, OICRs, Policies, and Innovations
  • I re-created the tip-submit and tip-approve DSpace user accounts for Alliance’s new TIP submit tool and added them to the Alliance submitters and Alliance admins accounts respectively
  • Start working on updating the Ansible infrastructure playbooks for DSpace 7 stuff

2022-07-23

2022-07-24

2022-07-25

  • More work on DSpace 7 related issues in the Ansible infrastructure playbooks
    • I see that, for Solr, we will need to copy the DSpace configsets to the writable data directory rather than the default home dir
    • The Taking Solr to production guide recommends keeping the unzipped code separate from the data, which we do in our Solr role already
    • So that means we keep the unzipped code in /opt/solr-8.11.2, but the data directory in /var/solr/data, with the DSpace Solr cores here /var/solr/data/configsets
    • I’m not sure how to integrate that into my playbooks yet
  • Much to my surprise, Discovery indexing on DSpace 7 was really fast when I did it just now, apparently taking 40 minutes of wall clock time?!:
$ /usr/bin/time -v /home/dspace7/bin/dspace index-discovery -b
The script has started
(Re)building index from scratch.
Done with indexing
The script has completed
        Command being timed: "/home/dspace7/bin/dspace index-discovery -b"
        User time (seconds): 588.18
        System time (seconds): 91.26
        Percent of CPU this job got: 28%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 40:05.79
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 635380
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 1513
        Minor (reclaiming a frame) page faults: 216412
        Voluntary context switches: 1671092
        Involuntary context switches: 744007
        Swaps: 0
        File system inputs: 4396880
        File system outputs: 74312
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0
  • Leroy from the Alliance wrote to say that the CIAT Library is back up so I might be able to download all the PDFs
    • It had been shut down for a security reason a few months ago and we were planning to download them all and attach them to their relevant items on CGSpace
    • I noticed one item that had the PDF already on CGSpace so I’ll need to consider that when I eventually do the import
  • I had to re-create the tip-submit and tip-approve accounts for Alliance on DSpace Test again
    • After I created them last week they somehow got deleted…?!… I couldn’t find them or the mel-submit account either!