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160 lines
8.7 KiB
Markdown
160 lines
8.7 KiB
Markdown
---
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title: "May, 2020"
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date: 2020-05-02T09:52:04+03:00
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author: "Alan Orth"
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categories: ["Notes"]
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---
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## 2020-05-02
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- Peter said that CTA is having problems submitting an item to CGSpace
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- 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
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- 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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<!--more-->
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## 2020-05-03
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- Purge a few remaining bots from CGSpace Solr statistics that I had identified a few months ago
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- `lua-resty-http/0.10 (Lua) ngx_lua/10000`
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- `omgili/0.5 +http://omgili.com`
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- `IZaBEE/IZaBEE-1.01 (Buzzing Abound The Web; https://izabee.com; info at izabee dot com)`
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- `Twurly v1.1 (https://twurly.org)`
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- `Pattern/2.6 +http://www.clips.ua.ac.be/pattern`
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- `CyotekWebCopy/1.7 CyotekHTTP/2.0`
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- 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
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- I noticed that our custom themes were incorrectly linking to the OpenSearch XML file
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- The bug [was fixed](https://jira.lyrasis.org/browse/DS-2592) for Mirage2 in 2015
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- Note that this did not prevent OpenSearch itself from working
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- I will patch this on our DSpace 5.x and 6.x branches
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## 2020-05-06
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- Atmire responded asking for more information about the Solr statistics processing bug in CUA so I sent them some full logs
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- 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.
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## 2020-05-07
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- Linode sent an alert that there was high CPU usage on CGSpace (linode18) early this morning
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- I looked at the nginx logs using goaccess and I found a few IPs making lots of requests around then:
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```
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# cat /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "07/May/2020:(01|03|04)" | goaccess --log-format=COMBINED -
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```
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- The two main IPs making requests around then are 188.134.31.88 and 212.34.8.188
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- 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
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- The second IP is CodeObia testing AReS, a total of 171,000 hits this month
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- I will purge both of those IPs from the Solr stats using my `check-spider-ip-hits.sh` script:
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```
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$ ./check-spider-ip-hits.sh -f /tmp/ips -s statistics -p
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Purging 171641 hits from 212.34.8.188 in statistics
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Purging 20691 hits from 188.134.31.88 in statistics
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Total number of bot hits purged: 192332
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```
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- 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
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- I also changed the nginx config to block requests with blank user agents
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## 2020-05-11
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- Bizu said she was having issues submitting to CGSpace last week
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- The issue sounds like the one Tezira and CTA were having in the last few weeks
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- I looked at the PostgreSQL graphs and see there are a lot of connections in "idle in transaction" and "waiting for lock" state:
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![PostgreSQL connections](/cgspace-notes/2020/05/postgres_connections_cgspace-week.png)
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- 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
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- Atmire sent some feedback about my ongoing issues with their CUA module, but none of it was conclusive yet
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- Regarding Font Awesome 5 they will check how much work it will take and give me a quote
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- 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
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- Last week Peter had asked me to add a new ILRI author's ORCID iD
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- 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:
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```
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$ cat 2020-05-11-add-orcids.csv
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dc.contributor.author,cg.creator.id
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"Lutakome, P.","Pius Lutakome: 0000-0002-0804-2649"
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"Lutakome, Pius","Pius Lutakome: 0000-0002-0804-2649"
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$ ./add-orcid-identifiers-csv.py -i 2020-05-11-add-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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```
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- Run system updates on CGSpace (linode18) and reboot it
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- I had to restart Tomcat five times before all Solr statistics cores came up OK, ugh.
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## 2020-05-12
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- Peter noticed that CGSpace is no longer on AReS, because I blocked all requests that don't specify a user agent
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- I've temporarily disabled that restriction and asked Moayad to look into how he can specify a user agent in the AReS harvester
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## 2020-05-13
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- Atmire responded about Font Awesome and said they can switch to version 5 for 16 credits
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- I told them to go ahead
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- 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
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- Run system updates and reboot AReS server (linode20) for the first time in almost 100 days
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- 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
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## 2020-05-17
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- Create an issue in the OpenRXV project for Moayad to change the default harvester user agent ([#36](https://github.com/ilri/OpenRXV/issues/36))
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## 2020-05-18
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- 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
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- I told them that they should try to run the code with the Solr statistics that I shared with them a few weeks ago
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## 2020-05-19
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- Add ORCID identifier for Sirak Bahta
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- 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:
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```
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$ cat 2020-05-19-add-orcids.csv
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dc.contributor.author,cg.creator.id
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"Bahta, Sirak T.","Sirak Bahta: 0000-0002-5728-2489"
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$ ./add-orcid-identifiers-csv.py -i 2020-05-19-add-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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```
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- 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:
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![PostgreSQL connections](/cgspace-notes/2020/05/postgres_connections_cgspace-week2.png)
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- 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)
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- I will downgrade it to version 42.2.9 for now...
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- The only other thing I can think of is that I upgraded Tomcat to 7.0.103 in March
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- Run system updates on DSpace Test (linode26) and reboot it
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- Run system updates on CGSpace (linode18) and reboot it
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- After the system came back up I had to restart Tomcat 7 three times before all the Solr statistics cores came up OK
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- Send Atmire a snapshot of the CGSpace database for them to possibly troubleshoot the CUA issue with DSpace 6
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## 2020-05-20
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- 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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## 2020-05-25
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- Add ORCID identifier for CIAT author Manuel Francisco
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- I added it to the controlled vocabulary and tagged the user's existing ~27 items in CGSpace using this CSV file with my `add-orcid-identifiers-csv.py` script:
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```
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$ cat 2020-05-25-add-orcids.csv
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dc.contributor.author,cg.creator.id
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"Díaz, Manuel F.","Manuel Francisco Diaz Baca: 0000-0001-8996-5092"
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"Díaz, Manuel Francisco","Manuel Francisco Diaz Baca: 0000-0001-8996-5092"
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$ ./add-orcid-identifiers-csv.py -i 2020-05-25-add-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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```
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- Last week Maria asked again about searching for items by accession or issue date
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- A few months ago I had told her to search for the ISO8601 date in Discovery search, which appears to work because it filters the results down quite a bit
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- She pointed out that the results include hits that don't exactly match, for example if part of the search string appears elsewhere like in the timestamp
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- I checked in Solr and the results are the same, so perhaps it's a limitation in Solr...?
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- So this effectively means that we don't have a way to create reports for items in an arbitrary date range shorter than a year:
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- DSpace advanced search is buggy or simply not designed to work like that
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- AReS Explorer currently only allows filtering by year, but will allow months soon
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- Atmire Listings and Reports only allows a "Timespan" of a year
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<!-- vim: set sw=2 ts=2: -->
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