cgspace-notes/content/posts/2020-05.md

---
title: "May, 2020"
date: 2020-05-02T09:52:04+03:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2020-05-02

- Peter said that CTA is having problems submitting an item to CGSpace
  - Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in 'idle in transaction' and 'waiting for lock' state are increasing again
  - I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)

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## 2020-05-03

- Purge a few remaining bots from CGSpace Solr statistics that I had identified a few months ago
  - `lua-resty-http/0.10 (Lua) ngx_lua/10000`
  - `omgili/0.5 +http://omgili.com`
  - `IZaBEE/IZaBEE-1.01 (Buzzing Abound The Web; https://izabee.com; info at izabee dot com)`
  - `Twurly v1.1 (https://twurly.org)`
  - `Pattern/2.6 +http://www.clips.ua.ac.be/pattern`
  - `CyotekWebCopy/1.7 CyotekHTTP/2.0`
- This is only about 2,500 hits total from the last ten years, and half of these bots no longer seem to exist, so I won't bother submitting them to the COUNTER-Robots project
- I noticed that our custom themes were incorrectly linking to the OpenSearch XML file
  - The bug [was fixed](https://jira.lyrasis.org/browse/DS-2592) for Mirage2 in 2015
  - Note that this did not prevent OpenSearch itself from working
  - I will patch this on our DSpace 5.x and 6.x branches

## 2020-05-06

- Atmire responded asking for more information about the Solr statistics processing bug in CUA so I sent them some full logs
  - Also I asked again about the Maven variable interpolation issue for `cua.version.number`, and if they would be willing to upgrade CUA to use Font Awesome 5 instead of 4.

## 2020-05-07

- Linode sent an alert that there was high CPU usage on CGSpace (linode18) early this morning
  - I looked at the nginx logs using goaccess and I found a few IPs making lots of requests around then:

```
# cat /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "07/May/2020:(01|03|04)" | goaccess --log-format=COMBINED -
```

- The two main IPs making requests around then are 188.134.31.88 and 212.34.8.188
  - The first is in Russia and it is hitting mostly XMLUI Discover links using _dozens_ of different user agents, a total of 20,000 requests this week
  - The second IP is CodeObia testing AReS, a total of 171,000 hits this month
  - I will purge both of those IPs from the Solr stats using my `check-spider-ip-hits.sh` script:

```
$ ./check-spider-ip-hits.sh -f /tmp/ips -s statistics -p
Purging 171641 hits from 212.34.8.188 in statistics
Purging 20691 hits from 188.134.31.88 in statistics

Total number of bot hits purged: 192332
```

- And then I will add 188.134.31.88 to the nginx bad bot list and tell CodeObia to please use a "bot" user agent
- I also changed the nginx config to block requests with blank user agents

## 2020-05-11

- Bizu said she was having issues submitting to CGSpace last week
  - The issue sounds like the one Tezira and CTA were having in the last few weeks
  - I looked at the PostgreSQL graphs and see there are a lot of connections in "idle in transaction" and "waiting for lock" state:

![PostgreSQL connections](/cgspace-notes/2020/05/postgres_connections_cgspace-week.png)

- I think I'll downgrade the PostgreSQL JDBC driver from 42.2.12 to 42.2.10, which was the version we were using before these issues started happening
- Atmire sent some feedback about my ongoing issues with their CUA module, but none of it was conclusive yet
  - Regarding Font Awesome 5 they will check how much work it will take and give me a quote
- Abenet said some users are questioning why the statistics dropped so much lately, so I made a [post to Yammer](https://www.yammer.com/dspacedevelopers/#/Threads/show?threadId=674923030216704) to explain about the robots
- Last week Peter had asked me to add a new ILRI author's ORCID iD
  - I added it to the controlled vocabulary and tagged the user's existing ~11 items in CGSpace using this CSV file with my `add-orcid-identifiers-csv.py` script:

```
$ cat 2020-05-11-add-orcids.csv
dc.contributor.author,cg.creator.id
"Lutakome, P.","Pius Lutakome: 0000-0002-0804-2649"
"Lutakome, Pius","Pius Lutakome: 0000-0002-0804-2649"
$ ./add-orcid-identifiers-csv.py -i 2020-05-11-add-orcids.csv -db dspace -u dspace -p 'fuuu' -d
```

- Run system updates on CGSpace (linode18) and reboot it
  - I had to restart Tomcat five times before all Solr statistics cores came up OK, ugh.

## 2020-05-12

- Peter noticed that CGSpace is no longer on AReS, because I blocked all requests that don't specify a user agent
  - I've temporarily disabled that restriction and asked Moayad to look into how he can specify a user agent in the AReS harvester

## 2020-05-13

- Atmire responded about Font Awesome and said they can switch to version 5 for 16 credits
  - I told them to go ahead
- Also, Atmire gave me a small workaround for the `cua.version.number` interpolation issue and said they would look into the crash that happens when processing our Solr stats
- Run system updates and reboot AReS server (linode20) for the first time in almost 100 days
  - I notice that AReS now has some of CGSpace's data in it (but not all) since I dropped the user-agent restriction on the REST API yesterday

## 2020-05-17

- Create an issue in the OpenRXV project for Moayad to change the default harvester user agent ([#36](https://github.com/ilri/OpenRXV/issues/36))

## 2020-05-18

- Atmire responded and said they still can't figure out the CUA statistics issue, though they seem to only be trying to understand what's going on using static analysis
  - I told them that they should try to run the code with the Solr statistics that I shared with them a few weeks ago

## 2020-05-19

- Add ORCID identifier for Sirak Bahta
  - I added it to the controlled vocabulary and tagged the user's existing ~40 items in CGSpace using this CSV file with my `add-orcid-identifiers-csv.py` script:

```
$ cat 2020-05-19-add-orcids.csv
dc.contributor.author,cg.creator.id
$ ./add-orcid-identifiers-csv.py -i 2020-05-19-add-orcids.csv -db dspace -u dspace -p 'fuuu' -d
"Bahta, Sirak T.","Sirak Bahta: 0000-0002-5728-2489"
```

- An IITA user is having issues submitting to CGSpace and I see there are a rising number of PostgreSQL connections waiting in transaction and in lock:

![PostgreSQL connections](/cgspace-notes/2020/05/postgres_connections_cgspace-week2.png)

- This is the same issue Tezira, Bizu, and CTA were having in the last few weeks and it I already downgraded the PostgreSQL JDBC driver version to the last version I was using before this started (42.2.10)
  - I will downgrade it to version 42.2.9 for now...
  - The only other thing I can think of is that I upgraded Tomcat to 7.0.103 in March
- Run system updates on DSpace Test (linode26) and reboot it
- Run system updates on CGSpace (linode18) and reboot it
  - After the system came back up I had to restart Tomcat 7 three times before all the Solr statistics cores came up OK
- Send Atmire a snapshot of the CGSpace database for them to possibly troubleshoot the CUA issue with DSpace 6

## 2020-05-20

- Send CodeObia some logos and footer text for the next phase of OpenRXV development ([#18](https://github.com/ilri/OpenRXV/issues/18))

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