July, 2022
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 toinput-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
):
- I found one host in Romania making very high speed requests with a normal user agent (
# 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
2022-07-07
- Finalize lists of non-AGROVOC subjects in CGSpace that I started last week
- I used the SQL helper functions to find the collections where each term was used:
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
)
- Bioversity subject (
- 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 removed these from the input-form.xml and Discovery facets: