CGSpace Notes

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

August, 2020

by Alan Orth in  Notes

2020-08-02

  • I spent a few days working on a Java-based curation task to tag items with ISO 3166-1 Alpha2 country codes based on their cg.coverage.country text values
    • It looks up the names in ISO 3166-1 first, and then in our CGSpace countries mapping (which has five or so of Peter’s preferred “display” country names)
    • It implements a “force” mode too that will clear existing country codes and re-tag everything
    • It is class based so I can easily add support for other vocabularies, and the technique could even be used for organizations with mappings to ROR and Clarisa…

2020-08-03

  • Atmire responded to the ticket about the ongoing upgrade issues
    • They pushed an RC2 version of the CUA module that fixes the FontAwesome issue so that they now use classes instead of Unicode hex characters so our JS + SVG works!
    • They also said they have never experienced the type: 5 site statistics issue, so I need to try to purge those and continue with the stats processing
  • I purged all unmigrated stats in a few cores and then restarted processing:
$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>id:/.*unmigrated.*/</query></delete>'
$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx2048m'
$ chrt -b 0 dspace dsrun com.atmire.statistics.util.update.atomic.AtomicStatisticsUpdateCLI -t 12 -c statistics
  • Andrea from Macaroni Bros emailed me a few days ago to say he’s having issues with the CGSpace REST API

2020-08-04

$ http 'http://localhost:8080/rest/collections/1445' | json_pp | grep numberItems
   "numberItems" : 63,
$ http 'http://localhost:8080/rest/collections/1445/items' jq '. | length'
61
  • Also on DSpace Test (which is running DSpace 6!), though the issue is slightly different there:
$ http 'https://dspacetest.cgiar.org/rest/collections/5471c3aa-202e-42f0-96c2-497a18e3b708' | json_pp | grep numberItems
   "numberItems" : 61,
$ http 'https://dspacetest.cgiar.org/rest/collections/5471c3aa-202e-42f0-96c2-497a18e3b708/items' | jq '. | length'
59
  • Ah! I exported that collection’s metadata and checked it in OpenRefine, where I noticed that two items are mapped twice
    • I dealt with this problem in 2017-01 and the solution is to check the collection2item table:
dspace=# SELECT * FROM collection2item WHERE item_id = '107687';
   id   | collection_id | item_id
--------+---------------+---------
 133698 |           966 |  107687
 134685 |          1445 |  107687
 134686 |          1445 |  107687
(3 rows)
  • So for each id you can delete one duplicate mapping:
dspace=# DELETE FROM collection2item WHERE id='134686';
dspace=# DELETE FROM collection2item WHERE id='128819';
  • Update countries on CGSpace to be closer to ISO 3166-1 with some minor differences based on Peter’s preferred display names
$ cat 2020-08-04-PB-new-countries.csv
cg.coverage.country,correct
CAPE VERDE,CABO VERDE
COCOS ISLANDS,COCOS (KEELING) ISLANDS
"CONGO, DR","CONGO, DEMOCRATIC REPUBLIC OF"
COTE D'IVOIRE,CÔTE D'IVOIRE
"KOREA, REPUBLIC","KOREA, REPUBLIC OF"
PALESTINE,"PALESTINE, STATE OF"
$ ./fix-metadata-values.py -i 2020-08-04-PB-new-countries.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.country -t 'correct' -m 228
  • I had to restart Tomcat 7 three times before all the Solr statistics cores came up properly
    • I started a full Discovery re-indexing

2020-08-05

  • Port my dspace-curation-tasks to DSpace 6 and tag version 6.0-SNAPSHOT
  • I downloaded the UN M.49 CSV file to start working on updating the CGSpace regions
    • First issue is they don’t version the file so you have no idea when it was released
    • Second issue is that three rows have errors due to not using quotes around “China, Macao Special Administrative Region”
  • Bizu said she was having problems approving tasks on CGSpace
    • I looked at the PostgreSQL locks and they have skyrocketed since yesterday:

PostgreSQL locks day

PostgreSQL query length day

  • Seems that something happened yesterday afternoon at around 5PM…
    • For now I will just run all updates on the server and reboot it, as I have no idea what causes this issue
    • I had to restart Tomcat 7 three times after the server came back up before all Solr statistics cores came up properly
  • I checked the nginx logs around 5PM yesterday to see who was accessing the server:
# cat /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E '04/Aug/2020:(17|18)' | goaccess --log-format=COMBINED -
  • I see the Macaroni Bros are using their new user agent for harvesting: RTB website BOT
    • But that pattern doesn’t match in the nginx bot list or Tomcat’s crawler session manager valve because we’re only checking for [Bb]ot!
    • So they have created thousands of Tomcat sessions:
$ cat dspace.log.2020-08-04 | grep -E "(63.32.242.35|64.62.202.71)" | grep -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
5693
  • DSpace itself uses a case-sensitive regex for user agents so there are no hits from those IPs in Solr, but I need to tweak the other regexes so they don’t misuse the resources
    • Perhaps [Bb][Oo][Tt]…
  • I see another IP 104.198.96.245, which is also using the “RTB website BOT” but there are 70,000 hits in Solr from earlier this year before they started using the user agent
    • I purged all the hits from Solr, including a few thousand from 64.62.202.71
  • A few more IPs causing lots of Tomcat sessions yesterday:
$ cat dspace.log.2020-08-04 | grep "38.128.66.10" | grep -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
1585
$ cat dspace.log.2020-08-04 | grep "64.62.202.71" | grep -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
5691
  • 38.128.66.10 isn’t creating any Solr statistics due to our DSpace agents pattern, but they are creating lots of sessions so perhaps I need to force them to use one session in Tomcat:
Mozilla/5.0 (Windows NT 5.1) brokenlinkcheck.com/1.2
  • 64.62.202.71 is using a user agent I’ve never seen before:
Mozilla/5.0 (compatible; +centuryb.o.t9[at]gmail.com)
  • So now our “bot” regex can’t even match that…
    • Unless we change it to [Bb]\.?[Oo]\.?[Tt]\.?… which seems to match all variations of “bot” I can think of right now, according to regexr.com:
RTB website BOT
Altmetribot
Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html)
Mozilla/5.0 (compatible; +centuryb.o.t9[at]gmail.com)
Mozilla/5.0 (compatible; BLEXBot/1.0; +http://webmeup-crawler.com/)
  • And another IP belonging to Turnitin (the alternate user agent of Turnitinbot):
$ cat dspace.log.2020-08-04 | grep "199.47.87.145" | grep -E 'sessi
on_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2777
  • I will add Turnitin to the Tomcat Crawler Session Manager Valve regex as well…

2020-08-06

  • I have been working on processing the Solr statistics with the Atmire tool on DSpace Test the last few days:
    • statistics:
      • 2,040,385 docs: 2h 28m 49s
    • statistics-2019:
      • 8,960,000 docs: 12h 7s
      • 1,780,575 docs: 2h 7m 29s
    • statistics-2018:
      • 1,970,000 docs: 12h 1m 28s
      • 360,000 docs: 2h 54m 56s (Linode rebooted)
      • 1,110,000 docs: 7h 1m 44s (Restarted Tomcat, oops)
  • I decided to start the 2018 core over again, so I re-synced it from CGSpace and started again from the solr-upgrade-statistics-6x tool and now I’m having the same issues with Java heap space that I had last month
    • The process kept crashing due to memory, so I increased the memory to 3072m and finally 4096m…
    • Also, I decided to try to purge all the -unmigrated docs that it had found so far to see if that helps…
    • There were about 466,000 records unmigrated so far, most of which were type: 5 (SITE statistics)
    • Now it is processing again…
  • I developed a small Java class called FixJpgJpgThumbnails to remove “.jpg.jpg” thumbnails from the THUMBNAIL bundle and replace them with their originals from the ORIGINAL bundle

2020-08-07

  • I improved the RemovePNGThumbnailsForPDFs.java a bit more to exclude infographics and original bitstreams larger than 100KiB
    • I ran it on CGSpace and it cleaned up 3,769 thumbnails!
    • Afterwards I ran dspace cleanup -v to remove the deleted thumbnails