CGSpace Notes

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

April, 2021

in  Notes

2021-04-01

  • I wrote a script to query Sherpa’s API for our ISSNs: sherpa-issn-lookup.py
    • I’m curious to see how the results compare with the results from Crossref yesterday
  • AReS Explorer was down since this morning, I didn’t see anything in the systemd journal
    • I simply took everything down with docker-compose and then back up, and then it was OK
    • Perhaps one of the containers crashed, I should have looked closer but I was in a hurry

2021-04-03

  • Biruk from ICT contacted me to say that some CGSpace users still can’t log in
    • I guess the CGSpace LDAP bind account is really still locked after last week’s reset
    • He fixed the account and then I was finally able to bind and query:
$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b "dc=cgiarad,dc=org" -D "cgspace-account" -W "(sAMAccountName=otheraccounttoquery)"

2021-04-04

  • Check the index aliases on AReS Explorer to make sure they are sane before starting a new harvest:
$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool | less
  • Then set the openrxv-items-final index to read-only so we can make a backup:
$ curl -X PUT "localhost:9200/openrxv-items-final/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}' 
{"acknowledged":true}%
$ curl -s -X POST http://localhost:9200/openrxv-items-final/_clone/openrxv-items-final-backup
{"acknowledged":true,"shards_acknowledged":true,"index":"openrxv-items-final-backup"}%
$ curl -X PUT "localhost:9200/openrxv-items-final/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
  • Then start a harvesting on AReS Explorer
  • Help Enrico get some 2020 statistics for the Roots, Tubers and Bananas (RTB) community on CGSpace
    • He was hitting a bug on AReS and also he only needed stats for 2020, and AReS currently only gives all-time stats
  • I cleaned up about 230 ISSNs on CGSpace in OpenRefine
    • I had exported them last week, then filtered for anything not looking like an ISSN with this GREL: isNotNull(value.match(/^\p{Alnum}{4}-\p{Alnum}{4}$/))
    • Then I applied them on CGSpace with the fix-metadata-values.py script:
$ ./ilri/fix-metadata-values.py -i /tmp/2021-04-01-ISSNs.csv -db dspace -u dspace -p 'fuuu' -f cg.issn -t 'correct' -m 253
  • For now I only fixed obvious errors like “1234-5678.” and “e-ISSN: 1234-5678” etc, but there are still lots of invalid ones which need more manual work:
    • Too few characters
    • Too many characters
    • ISBNs
  • Create the CGSpace community and collection structure for the new Accelerating Impacts of CGIAR Climate Research for Africa (AICCRA) and assign all workflow steps

2021-04-05

  • The AReS Explorer harvesting from yesterday finished, and the results look OK, but actually the Elasticsearch indexes are messed up again:
$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
{
    "openrxv-items-final": {
        "aliases": {}
    },
    "openrxv-items-temp": {
        "aliases": {
            "openrxv-items": {}
        }
    },
...
}
  • openrxv-items should be an alias of openrxv-items-final, not openrxv-temp… I will have to fix that manually
  • Enrico asked for more information on the RTB stats I gave him yesterday
    • I remembered (again) that we can’t filter Atmire’s CUA stats by date issued
    • To show, for example, views/downloads in the year 2020 for RTB issued in 2020, we would need to use the DSpace statistics API and post a list of IDs and a custom date range
    • I tried to do that here by exporting the RTB community and extracting the IDs for items issued in 2020:
$ ~/dspace63/bin/dspace metadata-export -i 10568/80100 -f /tmp/rtb.csv
$ csvcut -c 'id,dcterms.issued,dcterms.issued[],dcterms.issued[en_US]' /tmp/rtb.csv | \
  sed '1d' | \
  csvsql --no-header --no-inference --query 'SELECT a AS id,COALESCE(b, "")||COALESCE(c, "")||COALESCE(d, "") AS issued FROM stdin' | \
  csvgrep -c issued -m 2020 | \
  csvcut -c id | \
  sed '1d' | \
  sort | \
  uniq
  • So I remember in the future, this basically does the following:
    • Use csvcut to extract the id and all date issued columns from the CSV
    • Use sed to remove the header so we can refer to the columns using default a, b, c instead of their real names (which are tricky to match due to special characters)
    • Use csvsql to concatenate the various date issued columns (coalescing where null)
    • Use csvgrep to filter items by date issued in 2020
    • Use csvcut to extract the id column
    • Use sed to delete the header row
    • Use sort and uniq to filter out any duplicate IDs (there were three)
  • Then I have a list of 296 IDs for RTB items issued in 2020
  • I constructed a JSON file to post to the DSpace Statistics API:
{
  "limit": 100,
  "page": 0,
  "dateFrom": "2020-01-01T00:00:00Z",
  "dateTo": "2020-12-31T00:00:00Z",
  "items": [
"00358715-b70c-4fdd-aa55-730e05ba739e",
"004b54bb-f16f-4cec-9fbc-ab6c6345c43d",
"02fb7630-d71a-449e-b65d-32b4ea7d6904",
...
  ]
}
  • Then I submitted the file three times (changing the page parameter):
$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp > /tmp/page1.json
$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp > /tmp/page2.json
$ curl -s -d @/tmp/2020-items.txt https://cgspace.cgiar.org/rest/statistics/items | json_pp > /tmp/page3.json
  • Then I extracted the views and downloads in the most ridiculous way:
$ grep views /tmp/page*.json | grep -o -E '[0-9]+$' | sed 's/,//' | xargs | sed -e 's/ /+/g' | bc
30364
$ grep downloads /tmp/page*.json | grep -o -E '[0-9]+,' | sed 's/,//' | xargs | sed -e 's/ /+/g' | bc
9100
  • For curiousity I did the same exercise for items issued in 2019 and got the following:
    • Views: 30721
    • Downloads: 10205

2021-04-06

  • Margarita from CCAFS was having problems deleting an item from CGSpace again
    • The error was “Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:bd157345-448e …”
    • This is the same issue as last month
  • Create a new collection on CGSpace for a new CIP project at Mishel Portilla’s request
  • I got a notice that CGSpace was down
    • I didn’t see anything strange at first, but there are an insane amount of database connections:
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
12413
  • The system journal shows thousands of these messages in the system journal, this is the first one:
Apr 06 07:52:13 linode18 tomcat7[556]: Apr 06, 2021 7:52:13 AM org.apache.tomcat.jdbc.pool.ConnectionPool abandon
  • Around that time in the dspace log I see nothing unusual, but maybe these?
2021-04-06 07:52:29,409 INFO  com.atmire.dspace.cua.CUASolrLoggerServiceImpl @ Updating : 200/127 docs in http://localhost:8081/solr/statistics

$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
3640
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
2968
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
13
  • After ten minutes or so it went back down…
  • And now it’s back up in the thousands… I am seeing a lot of stuff in dspace log like this:
2021-04-06 11:59:34,364 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717951
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717952
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717953
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717954
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717955
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717956
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717957
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717958
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717959
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717960
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717961
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717962
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717963
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717964
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717965
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717966
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717967
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717968
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717969
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717970
2021-04-06 11:59:34,365 INFO  org.dspace.content.MetadataValueServiceImpl @ user.hidden@cgiar.org:session_id=65F32E67CE8E347F64EFB5EB4E349B9B:delete_metadata_value: metadata_value_id=5717971
  • I sent some notes and a log to Atmire on our existing issue about the database stuff
    • Also I asked them about the possibility of doing a formal review of Hibernate
  • Falcon 3.0.0 was released so I updated the 3.0.0 branch for dspace-statistics-api and merged it to v6_x
    • I also fixed one minor (unrelated) bug in the tests
    • Then I deployed the new version on DSpace Test
  • I had a meeting with Peter and Abenet about CGSpace TODOs
  • CGSpace went down again and the PostgreSQL locks are through the roof:
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
12154
  • I don’t see any activity on REST API, but in the last four hours there have been 3,500 DSpace sessions:
# grep -a -E '2021-04-06 (13|14|15|16|17):' /home/cgspace.cgiar.org/log/dspace.log.2021-04-06 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
3547
  • I looked at the same time of day for the past few weeks and it seems to be a normal number of sessions:
# for file in /home/cgspace.cgiar.org/log/dspace.log.2021-0{3,4}-*; do grep -a -E "2021-0(3|4)-[0-9]{2} (13|14|15|16|17):" "$file" | grep -o -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l; done
...
3572
4085
3476
3128
2949
2016
1839
4513
3463
4425
3328
2783
3898
3848
7799
255
534
2755
599
4463
3547
  • What about total number of sessions per day?
# for file in /home/cgspace.cgiar.org/log/dspace.log.2021-0{3,4}-*; do echo "$file:"; grep -a -o -E 'session_id=[A-Z0-9]{32}' "$file" | sort | uniq | wc -l; done
...
/home/cgspace.cgiar.org/log/dspace.log.2021-03-28:
11784
/home/cgspace.cgiar.org/log/dspace.log.2021-03-29:
15104
/home/cgspace.cgiar.org/log/dspace.log.2021-03-30:
19396
/home/cgspace.cgiar.org/log/dspace.log.2021-03-31:
32612
/home/cgspace.cgiar.org/log/dspace.log.2021-04-01:
26037
/home/cgspace.cgiar.org/log/dspace.log.2021-04-02:
14315
/home/cgspace.cgiar.org/log/dspace.log.2021-04-03:
12530
/home/cgspace.cgiar.org/log/dspace.log.2021-04-04:
13138
/home/cgspace.cgiar.org/log/dspace.log.2021-04-05:
16756
/home/cgspace.cgiar.org/log/dspace.log.2021-04-06:
12343
  • So it’s not the number of sessions… it’s something with the workload…
  • I had to step away for an hour or so and when I came back the site was still down and there were still 12,000 locks
    • I restarted postgresql and tomcat7…
  • The locks in PostgreSQL shot up again…
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
3447
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
3527
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
4582
  • I don’t know what the hell is going on, but the PostgreSQL connections and locks are way higher than ever before:

PostgreSQL connections week PostgreSQL locks week Tomcat database pool

  • Otherwise, the number of DSpace sessions is completely normal:

DSpace sessions

  • While looking at the nginx logs I see that MEL is trying to log into CGSpace’s REST API and delete items:
34.209.213.122 - - [06/Apr/2021:03:50:46 +0200] "POST /rest/login HTTP/1.1" 401 727 "-" "MEL"
34.209.213.122 - - [06/Apr/2021:03:50:48 +0200] "DELETE /rest/items/95f52bf1-f082-4e10-ad57-268a76ca18ec/metadata HTTP/1.1" 401 704 "-" "-"
  • I see a few of these per day going back several months
    • I sent a message to Salem and Enrico to ask if they know
  • Also annoying, I see tons of what look like penetration testing requests from Qualys:
2021-04-04 06:35:17,889 INFO  org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:failed_login:no DN found for user "'><qss a=X158062356Y1_2Z>
2021-04-04 06:35:17,889 INFO  org.dspace.authenticate.PasswordAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:authenticate:attempting password auth of user="'><qss a=X158062356Y1_2Z>
2021-04-04 06:35:17,890 INFO  org.dspace.app.xmlui.utils.AuthenticationUtil @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:failed_login:email="'><qss a=X158062356Y1_2Z>, realm=null, result=2
2021-04-04 06:35:18,145 INFO  org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:auth:attempting trivial auth of user=was@qualys.com
2021-04-04 06:35:18,519 INFO  org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:failed_login:no DN found for user was@qualys.com
2021-04-04 06:35:18,520 INFO  org.dspace.authenticate.PasswordAuthentication @ anonymous:session_id=FF1E051BCA7D81CC5A807D85380D81E5:ip_addr=64.39.108.48:authenticate:attempting password auth of user=was@qualys.com
  • I deleted the ilri/AReS repository on GitHub since we haven’t updated it in two years
  • 10PM and the server is down again, with locks through the roof:
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
12198
  • I see that there are tons of PostgreSQL connections getting abandoned today, compared to very few in the past few weeks:
$ journalctl -u tomcat7 --since=today | grep -c 'ConnectionPool abandon'
1838
$ journalctl -u tomcat7 --since=2021-03-20 --until=2021-04-05 | grep -c 'ConnectionPool abandon'
3
  • I even restarted the server and connections were low for a few minutes until they shot back up:
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
13
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
8651
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
8940
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
10504
  • I had to go to bed and I bet it will crash and be down for hours until I wake up…
  • What the hell is this user agent?
54.197.119.143 - - [06/Apr/2021:19:18:11 +0200] "GET /handle/10568/16499 HTTP/1.1" 499 0 "-" "GetUrl/1.0 wdestiny@umich.edu (Linux)"

2021-04-07

  • CGSpace was still down from last night of course, with tons of database locks:
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
12168
  • I restarted the server again and the locks came back
  • Atmire responded to the message from yesterday
    • The noticed something in the logs about emails failing to be sent
    • There appears to be an issue sending mails on workflow tasks when a user in that group has an invalid email address:
2021-04-01 12:45:11,414 WARN  org.dspace.workflowbasic.BasicWorkflowServiceImpl @ a.akwarandu@cgiar.org:session_id=2F20F20D4A8C36DB53D42DE45DFA3CCE:notifyGroupofTask:cannot email user group_id=aecf811b-b7e9-4b6f-8776-3d372e6a048b workflow_item_id=33085\colon;  Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException\colon; 501 5.1.3 Invalid address
  • The issue is not the named user above, but a member of the group…
  • And the group does have users with invalid email addresses (probably accounts created automatically after authenticating with LDAP):

DSpace group

  • I extracted all the group IDs from recent logs that had users with invalid email addresses:
$ grep -a -E 'email user group_id=\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' /home/cgspace.cgiar.org/log/dspace.log.* | grep -o -E '\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b' | sort | uniq
0a30d6ae-74a6-4eee-a8f5-ee5d15192ee6
1769137c-36d4-42b2-8fec-60585e110db7
203c8614-8a97-4ac8-9686-d9d62cb52acc
294603de-3d09-464e-a5b0-09e452c6b5ab
35878555-9623-4679-beb8-bb3395fdf26e
3d8a5efa-5509-4bf9-9374-2bc714aceb99
4238208a-f848-47cb-9dd2-43f9f954a4af
44939b84-1894-41e7-b3e6-8c8d1781057b
49ba087e-75a3-45ce-805c-69eeda0f786b
4a6606ce-0284-421d-bf80-4dafddba2d42
527de6aa-9cd0-4988-bf5f-c9c92ba2ac10
54cd1b16-65bf-4041-9d84-fb2ea3301d6d
58982847-5f7c-4b8b-a7b0-4d4de702136e
5f0b85be-bd23-47de-927d-bca368fa1fbc
646ada17-e4ef-49f6-9378-af7e58596ce1
7e2f4bf8-fbc9-4b2f-97a4-75e5427bef90
8029fd53-f9f5-4107-bfc3-8815507265cf
81faa934-c602-4608-bf45-de91845dfea7
8611a462-210c-4be1-a5bb-f87a065e6113
8855c903-ef86-433c-b0be-c12300eb0f84
8c7ece98-3598-4de7-a885-d61fd033bea8
8c9a0d01-2d12-4a99-84f9-cdc25ac072f9
8f9f888a-b501-41f3-a462-4da16150eebf
94168f0e-9f45-4112-ac8d-3ba9be917842
96998038-f381-47dc-8488-ff7252703627
9768f4a8-3018-44e9-bf58-beba4296327c
9a99e8d2-558e-4fc1-8011-e4411f658414
a34e6400-78ed-45c0-a751-abc039eed2e6
a9da5af3-4ec7-4a9b-becb-6e3d028d594d
abf5201c-8be5-4dee-b461-132203dd51cb
adb5658c-cef3-402f-87b6-b498f580351c
aecf811b-b7e9-4b6f-8776-3d372e6a048b
ba5aae61-ea34-4ac1-9490-4645acf2382f
bf7f3638-c7c6-4a8f-893d-891a6d3dafff
c617ada0-09d1-40ed-b479-1c4860a4f724
cff91d44-a855-458c-89e5-bd48c17d1a54
e65171ae-a2bf-4043-8f54-f8457bc9174b
e7098b40-4701-4ca2-b9a9-3a1282f67044
e904f122-71dc-439b-b877-313ef62486d7
ede59734-adac-4c01-8691-b45f19088d37
f88bd6bb-f93f-41cb-872f-ff26f6237068
f985f5fb-be5c-430b-a8f1-cf86ae4fc49a
fe800006-aaec-4f9e-9ab4-f9475b4cbdc3

2021-04-08

  • I can’t believe it but the server has been down for twelve hours or so
    • The locks have not changed since I went to bed last night:
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
12070
  • I restarted PostgreSQL and Tomcat and the locks go straight back up!
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
13
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
986
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
1194
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
1212
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
1489
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
2124
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
5934

2021-04-09

  • Atmire managed to get CGSpace back up by killing all the PostgreSQL connections yesterday
    • I don’t know how they did it…
    • They also think it’s weird that restarting PostgreSQL didn’t kill the connections
    • They asked some more questions, like for example if there were also issues on DSpace Test
    • Strangely enough, I checked DSpace Test and notice a clear spike in PostgreSQL locks on the morning of April 6th as well!

PostgreSQL locks week CGSpace PostgreSQL locks week DSpace Test

  • I definitely need to look into that!

2021-04-11

  • I am trying to resolve the AReS Elasticsearch index issues that happened last week
    • I decided to back up the openrxv-items index to openrxv-items-backup and then delete all the others:
$ curl -X PUT "localhost:9200/openrxv-items/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items-backup
$ curl -X PUT "localhost:9200/openrxv-items/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": false}}'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
  • Then I updated all Docker containers and rebooted the server (linode20) so that the correct indexes would be created again:
$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
  • Then I realized I have to clone the backup index directly to openrxv-items-final, and re-create the openrxv-items alias:
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
$ curl -X PUT "localhost:9200/openrxv-items-backup/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-backup/_clone/openrxv-items-final
$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
  • Now I see both openrxv-items-final and openrxv-items have the current number of items:
$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty'     
{
  "count" : 103373,
  "_shards" : {
    "total" : 1,
    "successful" : 1,
    "skipped" : 0,
    "failed" : 0
  }
}
$ curl -s 'http://localhost:9200/openrxv-items-final/_count?q=*&pretty'
{
  "count" : 103373,
  "_shards" : {
    "total" : 1,
    "successful" : 1,
    "skipped" : 0,
    "failed" : 0
  }
}
  • Then I started a fresh harvesting in the AReS Explorer admin dashboard

2021-04-12

  • The harvesting on AReS finished last night, but the indexes got messed up again
    • I will have to fix them manually next time…

2021-04-13

  • Looking into the logs on 2021-04-06 on CGSpace and DSpace Test to see if there is anything specific that stands out about the activty on those days that would cause the PostgreSQL issues
    • Digging into the Munin graphs for the last week I found a few other things happening on that morning:

/dev/sda disk latency week JVM classes unloaded week Nginx status week

  • 13,000 requests in the last two months from a user with user agent SomeRandomText, for example:
84.33.2.97 - - [06/Apr/2021:06:25:13 +0200] "GET /bitstream/handle/10568/77776/CROP%20SCIENCE.jpg.jpg HTTP/1.1" 404 10890 "-" "SomeRandomText"
  • I purged them:
$ ./ilri/check-spider-hits.sh -f /tmp/agents.txt -p
Purging 13159 hits from SomeRandomText in statistics

Total number of bot hits purged: 13159
  • I noticed there were 78 items submitted in the hour before CGSpace crashed:
# grep -a -E '2021-04-06 0(6|7):' /home/cgspace.cgiar.org/log/dspace.log.2021-04-06 | grep -c -a add_item 
78
  • Of those 78, 77 of them were from Udana
  • Compared to other mornings (0 to 9 AM) this month that seems to be pretty high:
# for num in {01..13}; do grep -a -E "2021-04-$num 0" /home/cgspace.cgiar.org/log/dspace.log.2021-04-$num | grep -c -a
 add_item; done
32
0
0
2
8
108
4
0
29
0
1
1
2

2021-04-15

  • Release v1.4.2 of the DSpace Statistics API on GitHub: https://github.com/ilri/dspace-statistics-api/releases/tag/v1.4.2
    • This has been running on DSpace Test for the last week or so, and mostly contains the Falcon 3.0.0 changes
  • Re-sync DSpace Test with data from CGSpace
    • Run system updates on DSpace Test (linode26) and reboot the server
  • Update the PostgreSQL JDBC driver on DSpace Test (linode26) to 42.2.19
    • It has been a few months since we updated this, and there have been a few releases since 42.2.14 that we are currently using
  • Create a test account for Rafael from Bioversity-CIAT to submit some items to DSpace Test:
$ dspace user -a -m tip-submit@cgiar.org -g CIAT -s Submit -p 'fuuuuuuuu'
  • I added the account to the Alliance Admins account, which is should allow him to submit to any Alliance collection
    • According to my notes from 2020-10 the account must be in the admin group in order to submit via the REST API

2021-04-18

  • Update all containers on AReS (linode20):
$ docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | xargs -L1 docker pull
  • Then run all system updates and reboot the server
  • I learned a new command for Elasticsearch:
$ curl http://localhost:9200/_cat/indices
yellow open openrxv-values           ChyhGwMDQpevJtlNWO1vcw 1 1   1579      0 537.6kb 537.6kb
yellow open openrxv-items-temp       PhV5ieuxQsyftByvCxzSIw 1 1 103585 104372 482.7mb 482.7mb
yellow open openrxv-shared           J_8cxIz6QL6XTRZct7UBBQ 1 1    127      0 115.7kb 115.7kb
yellow open openrxv-values-00001     jAoXTLR0R9mzivlDVbQaqA 1 1   3903      0 696.2kb 696.2kb
green  open .kibana_task_manager_1   O1zgJ0YlQhKCFAwJZaNSIA 1 0      2      2  20.6kb  20.6kb
yellow open openrxv-users            1hWGXh9kS_S6YPxAaBN8ew 1 1      5      0  28.6kb  28.6kb
green  open .apm-agent-configuration f3RAkSEBRGaxJZs3ePVxsA 1 0      0      0    283b    283b
yellow open openrxv-items-final      sgk-s8O-RZKdcLRoWt3G8A 1 1    970      0   2.3mb   2.3mb
green  open .kibana_1                HHPN7RD_T7qe0zDj4rauQw 1 0     25      7  36.8kb  36.8kb
yellow open users                    M0t2LaZhSm2NrF5xb64dnw 1 1      2      0  11.6kb  11.6kb
  • Somehow the openrxv-items-final index only has a few items and the majority are in openrxv-items-temp, via the openrxv-items alias (which is in the temp index):
$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty' 
{
  "count" : 103585,
  "_shards" : {
    "total" : 1,
    "successful" : 1,
    "skipped" : 0,
    "failed" : 0
  }
}
  • I found a cool tool to help with exporting and restoring Elasticsearch indexes:
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --limit=1000 --type=data
...
Sun, 18 Apr 2021 06:27:07 GMT | Total Writes: 103585
Sun, 18 Apr 2021 06:27:07 GMT | dump complete
  • It took only two or three minutes to export everything…
  • I did a test to restore the index:
$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-test --type=mapping
$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items-test --limit 1000 --type=data
  • So that’s pretty cool!
  • I deleted the openrxv-items-final index and openrxv-items-temp indexes and then restored the mappings to openrxv-items-final, added the openrxv-items alias, and started restoring the data to openrxv-items with elasticdump:
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items --limit 1000 --type=data
  • AReS seems to be working fine аfter that, so I created the openrxv-items-temp index and then started a fresh harvest on AReS Explorer:
$ curl -X PUT "localhost:9200/openrxv-items-temp"
  • Run system updates on CGSpace (linode18) and run the latest Ansible infrastructure playbook to update the DSpace Statistics API, PostgreSQL JDBC driver, etc, and then reboot the system
  • I wasted a bit of time trying to get TSLint and then ESLint running for OpenRXV on GitHub Actions

2021-04-19

  • The AReS harvesting last night seems to have completed successfully, but the number of results is strange:
$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
yellow open openrxv-items-temp       kNUlupUyS_i7vlBGiuVxwg 1 1 103741 105553 483.6mb 483.6mb
yellow open openrxv-items-final      HFc3uytTRq2GPpn13vkbmg 1 1    970      0   2.3mb   2.3mb
  • The indices endpoint doesn’t include the openrxv-items alias, but it is currently in the openrxv-items-temp index so the number of items is the same:
$ curl -s 'http://localhost:9200/openrxv-items/_count?q=*&pretty'     
{
  "count" : 103741,
  "_shards" : {
    "total" : 1,
    "successful" : 1,
    "skipped" : 0,
    "failed" : 0
  }
}
  • A user was having problems resetting their password on CGSpace, with some message about SMTP etc
    • I checked and we are indeed locked out of our mailbox:
$ dspace test-email
...
Error sending email:
 - Error: javax.mail.SendFailedException: Send failure (javax.mail.AuthenticationFailedException: 550 5.2.1 Mailbox cannot be accessed [PR0P264CA0280.FRAP264.PROD.OUTLOOK.COM]
)

2021-04-21

  • Send Abdullah feedback on the filter on click pull request for OpenRXV
    • I see it adds a new “allow filter on click” checkbox in the layout settings, but it doesn’t modify the filters
    • Also, it seems to have broken the existing clicking of the countries on the map
  • Atmire recently sent feedback about the CUA duplicates processor
    • Last month when I ran it it got stuck on the storage reports, apparently, so I will try again (with a fresh Solr statistics core from production) and skip the storage reports (-g):
$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
$ cp atmire-cua-update.xml-20210124-132112.old /home/dspacetest.cgiar.org/config/spring/api/atmire-cua-update.xml
$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -r 100 -c statistics -t 12 -g
  • The first run processed 1,439 docs, the second run processed 0 docs
    • I’m not sure if that means that it worked? I sent feedback to Atmire
  • Meeting with Moayad to discuss OpenRXV development progress

2021-04-25

  • The indexes on AReS are messed up again
    • I made a backup of the indexes, then deleted the openrxv-items-final and openrxv-items-temp indexes, re-created the openrxv-items alias, and restored the data into openrxv-items:
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_mapping.json --type=mapping
$ elasticdump --input=http://localhost:9200/openrxv-items --output=/home/aorth/openrxv-items_data.json --limit=1000 --type=data
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-final'
$ elasticdump --input=/home/aorth/openrxv-items_mapping.json --output=http://localhost:9200/openrxv-items-final --type=mapping
$ curl -s -X POST 'http://localhost:9200/_aliases' -H 'Content-Type: application/json' -d'{"actions" : [{"add" : { "index" : "openrxv-items-final", "alias" : "openrxv-items"}}]}'
$ elasticdump --input=/home/aorth/openrxv-items_data.json --output=http://localhost:9200/openrxv-items --limit 1000 --type=data
  • Then I started a fresh AReS harvest

2021-04-26

  • The AReS harvest last night seems to have finished successfully and the number of items looks good:
$ curl -s http://localhost:9200/_cat/indices | grep openrxv-items
yellow open openrxv-items-temp       H-CGsyyLTaqAj6-nKXZ-7w 1 1      0 0    283b    283b
yellow open openrxv-items-final      ul3SKsa7Q9Cd_K7qokBY_w 1 1 103951 0   254mb   254mb
  • And the aliases seem correct for once:
$ curl -s 'http://localhost:9200/_alias/' | python -m json.tool
...
    "openrxv-items-final": {
        "aliases": {
            "openrxv-items": {}
        }
    },
    "openrxv-items-temp": {
        "aliases": {}
    },
...
  • That’s 250 new items in the index since the last harvest!
  • Re-create my local Artifactory container because I’m getting errors starting it and it has been a few months since it was updated:
$ podman rm artifactory
$ podman pull docker.bintray.io/jfrog/artifactory-oss:latest
$ podman create --ulimit nofile=32000:32000 --name artifactory -v artifactory_data:/var/opt/jfrog/artifactory -p 8081-8082:8081-8082 docker.bintray.io/jfrog/artifactory-oss
$ podman start artifactory
  • Start testing DSpace 7.0 Beta 5 so I can evaluate if it solves some of the problems we are having on DSpace 6, and if it’s missing things like multiple handle resolvers, etc
    • I see it needs Java JDK 11, Tomcat 9, Solr 8, and PostgreSQL 11
    • Also, according to the installation notes I see you can install the old DSpace 6 REST API, so that’s potentially useful for us
    • I see that all web applications on the backend are now rolled into just one “server” application
    • The build process took 11 minutes the first time (due to downloading the world with Maven) and ~2 minutes the second time
    • The local.cfg content and syntax is very similar DSpace 6
  • I got the basic fresh_install up and running
    • Then I tried to import a DSpace 6 database from production
  • I tried to delete all the Atmire SQL migrations:
localhost/dspace7b5= > DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%';
  • But I got an error when running dspace database migrate:
$ ~/dspace7b5/bin/dspace database migrate

Database URL: jdbc:postgresql://localhost:5432/dspace7b5
Migrating database to latest version... (Check dspace logs for details)
Migration exception:
java.sql.SQLException: Flyway migration error occurred
        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:738)
        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:632)
        at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:228)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:273)
        at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:129)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:94)
Caused by: org.flywaydb.core.api.FlywayException: Validate failed: 
Detected applied migration not resolved locally: 5.0.2017.09.25
Detected applied migration not resolved locally: 6.0.2017.01.30
Detected applied migration not resolved locally: 6.0.2017.09.25

        at org.flywaydb.core.Flyway.doValidate(Flyway.java:292)
        at org.flywaydb.core.Flyway.access$100(Flyway.java:73)
        at org.flywaydb.core.Flyway$1.execute(Flyway.java:166)
        at org.flywaydb.core.Flyway$1.execute(Flyway.java:158)
        at org.flywaydb.core.Flyway.execute(Flyway.java:527)
        at org.flywaydb.core.Flyway.migrate(Flyway.java:158)
        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:729)
        ... 9 more
  • I deleted those migrations:
localhost/dspace7b5= > DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25');
  • Then when I ran the migration again it failed for a new reason, related to the configurable workflow:
Database URL: jdbc:postgresql://localhost:5432/dspace7b5
Migrating database to latest version... (Check dspace logs for details)
Migration exception:
java.sql.SQLException: Flyway migration error occurred
        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:738)
        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:632)
        at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:228)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:273)
        at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:129)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:94)
Caused by: org.flywaydb.core.internal.command.DbMigrate$FlywayMigrateException:
Migration V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql failed
--------------------------------------------------------------------
SQL State  : 42P01
Error Code : 0
Message    : ERROR: relation "cwf_pooltask" does not exist
  Position: 8
Location   : org/dspace/storage/rdbms/sqlmigration/postgres/V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql (/home/aorth/src/apache-tomcat-9.0.45/file:/home/aorth/dspace7b5/lib/dspace-api-7.0-beta5.jar!/org/dspace/storage/rdbms/sqlmigration/postgres/V7.0_2019.05.02__DS-4239-workflow-xml-migration.sql)
Line       : 16
Statement  : UPDATE cwf_pooltask SET workflow_id='defaultWorkflow' WHERE workflow_id='default'
...

$ ~/dspace7b5/bin/dspace database migrate ignored
  • Now I see all migrations have completed and DSpace actually starts up fine!
  • I will try to do a full re-index to see how long it takes:
$ time ~/dspace7b5/bin/dspace index-discovery -b
...
~/dspace7b5/bin/dspace index-discovery -b  25156.71s user 64.22s system 97% cpu 7:11:09.94 total
  • Not good, that shit took almost seven hours!

2021-04-27

  • Peter sent me a list of 500+ DOIs from CGSpace with no Altmetric score
    • I used csvgrep (with Windows encoding!) to extract those without our handle and save the DOIs to a text file, then got their handles with my doi-to-handle.py script:
$ csvgrep -e 'windows-1252' -c 'Handle.net IDs' -i -m '10568/' ~/Downloads/Altmetric\ -\ Research\ Outputs\ -\ CGSpace\ -\ 2021-04-26.csv | csvcut -c DOI | sed '1d' > /tmp/dois.txt
$ ./ilri/doi-to-handle.py -i /tmp/dois.txt -o /tmp/handles.csv -db dspace63 -u dspace -p 'fuuu' -d
  • He will Tweet them…

2021-04-28

  • Grant some IWMI colleagues access to the Atmire Content and Usage stats on CGSpace