CGSpace 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

• There is a great blog post discussing Soundex with Levenshtein and creating indexes to make them faster
• I want to do some proper checks of accuracy and speed against my trigram method

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

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

• 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