cgspace-notes/content/posts/2021-12.md

---
title: "December, 2021"
date: 2021-12-01T16:07:07+02:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2021-12-01

- Atmire merged some changes I had submitted to the COUNTER-Robots project
- I updated our local spider user agents and then re-ran the list with my `check-spider-hits.sh` script on CGSpace:

```console
$ ./ilri/check-spider-hits.sh -f /tmp/agents -p  
Purging 1989 hits from The Knowledge AI in statistics
Purging 1235 hits from MaCoCu in statistics
Purging 455 hits from WhatsApp in statistics

Total number of bot hits purged: 3679
```

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## 2021-12-02

- Francesca from Alliance asked me for help with approving a submission that gets stuck
  - I looked at the PostgreSQL activity and the locks are back up like they were earlier this week

```console
$ psql -c "SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" | sort | uniq -c | sort -n
      1 
      1 ------------------
      1 (1437 rows)
      1  application_name 
      9  psql
   1428  dspaceWeb
```

- Munin shows the same:

![PostgreSQL locks week](/cgspace-notes/2021/12/postgres_locks_ALL-week.png)

- Last month I enabled the `log_lock_waits` in PostgreSQL so I checked the log and was surprised to find only a few since I restarted PostgreSQL three days ago:

```console
# grep -E '^2021-(11-29|11-30|12-01|12-02)' /var/log/postgresql/postgresql-10-main.log | grep -c 'still waiting for'
15
```

- I think you could analyze the locks for the `dspaceWeb` user (XMLUI) and find out what queries were locking... but it's so much information and I don't know where to start
  - For now I just restarted PostgreSQL...
  - Francesca was able to do her submission immediately...
- On a related note, I want to enable the `pg_stat_statement` feature to see which queries get run the most, so I created the extension on the CGSpace database
- I was doing some research on PostgreSQL locks and found some interesting things to consider
  - The default `lock_timeout` is 0, aka disabled
  - The default `statement_timeout` is 0, aka disabled
  - It seems to be recommended to start by setting `statement_timeout` first, rule of thumb [ten times longer than your longest query](https://github.com/jberkus/annotated.conf/blob/master/postgresql.10.simple.conf#L211)
- Mark Wood mentioned the `checker` cron job that apparently runs in one transaction and might be an issue
  - I definitely saw it holding a bunch of locks for ~30 minutes during the first part of its execution, then it dropped them and did some other less-intensive things without locks
- Bizuwork was still not receiving emails even after we fixed the SMTP access on CGSpace
  - After some troubleshooting it turns out that the emails from CGSpace were going in her Junk!

## 2021-12-03

- I see GARDIAN is now using a "GARDIAN" user agent finally
  - I will add them to our local spider agent override in DSpace so that the hits don't get counted in Solr

## 2021-12-05

- Proof fifty records Abenet sent me from Africa Rice Center ("AfricaRice 1st batch Import")
  - Fixed forty-six incorrect collections
  - Cleaned up and normalize affiliations
  - Cleaned up dates (extra `*` character in all?)
  - Cleaned up citation format
  - Fixed some encoding issues in abstracts
  - Removed empty columns
  - Removed one duplicate: Enhancing Rice Productivity and Soil Nitrogen Using Dual-Purpose Cowpea-NERICA® Rice Sequence in Degraded Savanna
  - Added volume and issue metadata by extracting it from the citations
  - All PDFs hosted on davidpublishing.com are dead...
  - All DOIs linking to African Journal of Agricultural Research are dead...
  - Fixed a handful of items marked as "Open Access" that are actually closed
  - Added many missing ISSNs
  - Added many missing countries/regions
  - Fixed invalid AGROVOC terms and added some more based on article subjects
- I also made some minor changes to the [CSV Metadata Quality Checker](https://github.com/ilri/csv-metadata-quality)
  - Added the ability to check if the item's title exists in the citation
  - Updated to only run the mojibake check if we're not running in unsafe mode (so we don't print the same warning during both the check and fix steps)
- I ran the re-harvesting on AReS

## 2021-12-06

- Some minor work on the `check-duplicates.py` script I wrote last month
  - I found some corner cases where there were items that matched in the database, but they were `in_archive=f` and or `withdrawn=t` so I check that before trying to resolve the handles of potential duplicates
- More work on the Africa Rice Center 1st batch import
  - I merged the metadata for three duplicates in Africa Rice's items and mapped them on CGSpace
  - I did a bit more work to add missing AGROVOC subjects, countries, regions, extents, etc and then uploaded the forty-six items to CGSpace
- I started looking at the seventy CAS records that Abenet has been working on for the past few months

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