July, 2022

Sat Jul 02, 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

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

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
- They apparently publish a list of all their networks
- I wrote a script to use prips to print the IPs for each network
- The script is bing-networks-to-ips.sh
- From Bing’s IPs alone I purged 145,403 hits… sheesh
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