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Add notes for 2018-02-01
2018-02-01 15:30:28 +01:00
---
title: "February, 2018"
date: 2018-02-01T16:28:54+02:00
author: "Alan Orth"
tags: ["Notes"]
---
## 2018-02-01
- Peter gave feedback on the `dc.rights` proof of concept that I had sent him last week
- We don't need to distinguish between internal and external works, so that makes it just a simple list
Update notes
2018-02-01 18:04:07 +01:00
- Yesterday I figured out how to monitor DSpace sessions using JMX
- I copied the logic in the `jmx_tomcat_dbpools` provided by Ubuntu's `munin-plugins-java` package and used the stuff I discovered about JMX [in 2018-01]({{< relref "2018-01.md" >}})
Add notes for 2018-02-01
2018-02-01 15:30:28 +01:00
<!--more-->
Update notes
2018-02-01 18:04:07 +01:00
![DSpace Sessions](/cgspace-notes/2018/02/jmx_dspace_sessions-day.png)
- Run all system updates and reboot DSpace Test
- Wow, I packaged up the `jmx_dspace_sessions` stuff in the [Ansible infrastructure scripts](https://github.com/ilri/rmg-ansible-public) and deployed it on CGSpace and it totally works:
```
# munin-run jmx_dspace_sessions
v_.value 223
v_jspui.value 1
v_oai.value 0
```
Updates
2018-02-03 08:44:31 +01:00
## 2018-02-03
- Bram from Atmire responded about the high load caused by the Solr updater script and said it will be fixed with the updates to DSpace 5.8 compatibility: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=566
- We will close that ticket for now and wait for the 5.8 stuff: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560
Update notes
2018-02-03 23:00:51 +01:00
- I finally took a look at the second round of cleanups Peter had sent me for author affiliations in mid January
- After trimming whitespace and quickly scanning for encoding errors I applied them on CGSpace:
```
$ ./delete-metadata-values.py -i /tmp/2018-02-03-Affiliations-12-deletions.csv -f cg.contributor.affiliation -m 211 -d dspace -u dspace -p 'fuuu'
$ ./fix-metadata-values.py -i /tmp/2018-02-03-Affiliations-1116-corrections.csv -f cg.contributor.affiliation -t correct -m 211 -d dspace -u dspace -p 'fuuu'
```
- Then I started a full Discovery reindex:
```
$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
Update notes
2018-02-04 10:26:07 +01:00
real 96m39.823s
user 14m10.975s
sys 2m29.088s
Update notes
2018-02-03 23:00:51 +01:00
```
- Generate a new list of affiliations for Peter to sort through:
```
dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'affiliation') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/affiliations.csv with csv;
COPY 3723
```
- Oh, and it looks like we processed over 3.1 million requests in January, up from 2.9 million in [December]({{< relref "2017-12.md" >}}):
```
# time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Jan/2018"
3126109
real 0m23.839s
user 0m27.225s
sys 0m1.905s
```
Update notes
2018-02-05 18:08:05 +01:00
## 2018-02-05
- Toying with correcting authors with trailing spaces via PostgreSQL:
```
dspace=# update metadatavalue set text_value=REGEXP_REPLACE(text_value, '\s+$' , '') where resource_type_id=2 and metadata_field_id=3 and text_value ~ '^.*?\s+$';
UPDATE 20
```
- I tried the `TRIM(TRAILING from text_value)` function and it said it changed 20 items but the spaces didn't go away
- This is on a fresh import of the CGSpace database, but when I tried to apply it on CGSpace there were no changes detected. Weird.
- Anyways, Peter wants a new list of authors to clean up, so I exported another CSV:
```
dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors-2018-02-05.csv with csv;
COPY 55630
```
Add notes for 2018-02-06
2018-02-06 13:03:07 +01:00
## 2018-02-06
- UptimeRobot says CGSpace is down this morning around 9:15
- I see 308 PostgreSQL connections in `pg_stat_activity`
- The usage otherwise seemed low for REST/OAI as well as XMLUI in the last hour:
```
# date
Tue Feb 6 09:30:32 UTC 2018
# cat /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E "6/Feb/2018:(08|09)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
2 223.185.41.40
2 66.249.64.14
2 77.246.52.40
4 157.55.39.82
4 193.205.105.8
5 207.46.13.63
5 207.46.13.64
6 154.68.16.34
7 207.46.13.66
1548 50.116.102.77
# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 /var/log/nginx/error.log /var/log/nginx/error.log.1 | grep -E "6/Feb/2018:(08|09)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
77 213.55.99.121
86 66.249.64.14
101 104.196.152.243
103 207.46.13.64
118 157.55.39.82
133 207.46.13.66
136 207.46.13.63
156 68.180.228.157
295 197.210.168.174
752 144.76.64.79
```
- I did notice in `/var/log/tomcat7/catalina.out` that Atmire's update thing was running though
- So I restarted Tomcat and now everything is fine
- Next time I see that many database connections I need to save the output so I can analyze it later
- I'm going to re-schedule the taskUpdateSolrStatsMetadata task as [Bram detailed in ticket 566](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=566) to see if it makes CGSpace stop crashing every morning
- If I move the task from 3AM to 3PM, deally CGSpace will stop crashing in the morning, or start crashing ~12 hours later
- Eventually Atmire has said that there will be a fix for this high load caused by their script, but it will come with the 5.8 compatability they are already working on
- I re-deployed CGSpace with the new task time of 3PM, ran all system updates, and restarted the server
- Also, I changed the name of the DSpace fallback pool on DSpace Test and CGSpace to be called 'dspaceCli' so that I can distinguish it in `pg_stat_activity`
- I implemented some changes to the pooling in the [Ansible infrastructure scripts](https://github.com/ilri/rmg-ansible-public) so that each DSpace web application can use its own pool (web, api, and solr)
- Each pool uses its own name and hopefully this should help me figure out which one is using too many connections next time CGSpace goes down
- Also, this will mean that when a search bot comes along and hammers the XMLUI, the REST and OAI applications will be fine
- I'm not actually sure if the Solr web application uses the database though, so I'll have to check later and remove it if necessary
Update notes for 2018-02-06
2018-02-06 13:03:46 +01:00
- I deployed the changes on DSpace Test only for now, so I will monitor and make them on CGSpace later this week
Add notes for 2018-02-07
2018-02-07 11:34:36 +01:00
## 2018-02-07
- Abenet wrote to ask a question about the ORCiD lookup not working for one CIAT user on CGSpace
- I tried on DSpace Test and indeed the lookup just doesn't work!
- The ORCiD code in DSpace appears to be using `http://pub.orcid.org/`, but when I go there in the browser it redirects me to `https://pub.orcid.org/v2.0/`
- According to [the announcement](https://groups.google.com/forum/#!topic/orcid-api-users/qfg-HwAB1bk) the v1 API was moved from `http://pub.orcid.org/` to `https://pub.orcid.org/v1.2` until March 1st when it will be discontinued for good
- But the old URL is hard coded in DSpace and it doesn't work anyways, because it currently redirects you to `https://pub.orcid.org/v2.0/v1.2`
- So I guess we have to disable that shit once and for all and switch to a controlled vocabulary
Update notes for 2018-02-07
2018-02-07 17:33:26 +01:00
- CGSpace crashed again, this time around `Wed Feb 7 11:20:28 UTC 2018`
- I took a few snapshots of the PostgreSQL activity at the time and as the minutes went on and the connections were very high at first but reduced on their own:
```
$ psql -c 'select * from pg_stat_activity' > /tmp/pg_stat_activity.txt
$ grep -c 'PostgreSQL JDBC' /tmp/pg_stat_activity*
/tmp/pg_stat_activity1.txt:300
/tmp/pg_stat_activity2.txt:272
/tmp/pg_stat_activity3.txt:168
/tmp/pg_stat_activity4.txt:5
/tmp/pg_stat_activity5.txt:6
```
- Interestingly, all of those 751 connections were idle!
```
$ grep "PostgreSQL JDBC" /tmp/pg_stat_activity* | grep -c idle
751
```
- Since I was restarting Tomcat anyways, I decided to deploy the changes to create two different pools for web and API apps
- Looking the Munin graphs, I can see that there were almost double the normal number of DSpace sessions at the time of the crash (and also yesterday!):
![DSpace Sessions](/cgspace-notes/2018/02/jmx_dspace-sessions-day.png)
- Indeed it seems like there were over 1800 sessions today around the hours of 10 and 11 AM:
```
$ grep -E '^2018-02-07 (10|11)' dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
1828
```
- CGSpace went down again a few hours later, and now the connections to the dspaceWeb pool are maxed at 250 (the new limit I imposed with the new separate pool scheme)
- What's interesting is that the DSpace log says the connections are all busy:
```
org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-328] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:250; busy:250; idle:0; lastwait:5000].
```
- ... but in PostgreSQL I see them `idle` or `idle in transaction`:
```
$ psql -c 'select * from pg_stat_activity' | grep -c dspaceWeb
250
$ psql -c 'select * from pg_stat_activity' | grep dspaceWeb | grep -c idle
250
$ psql -c 'select * from pg_stat_activity' | grep dspaceWeb | grep -c "idle in transaction"
187
```
- What the fuck, does DSpace think all connections are busy?
- I suspect these are issues with abandoned connections or maybe a leak, so I'm going to try adding the `removeAbandoned='true'` parameter which is apparently off by default
- I will try `testOnReturn='true'` too, just to add more validation, because I'm fucking grasping at straws
Update notes for 2018-02-07
2018-02-07 17:34:39 +01:00
- Also, WTF, there was a heap space error randomly in catalina.out:
```
Wed Feb 07 15:01:54 UTC 2018 | Query:containerItem:91917 AND type:2
Exception in thread "http-bio-127.0.0.1-8081-exec-58" java.lang.OutOfMemoryError: Java heap space
```
Update notes for 2018-02-07
2018-02-07 23:55:28 +01:00
- I'm trying to find a way to determine what was using all those Tomcat sessions, but parsing the DSpace log is hard because some IPs are IPv6, which contain colons!
- Looking at the first crash this morning around 11, I see these IPv4 addresses making requests around 10 and 11AM:
```
$ grep -E '^2018-02-07 (10|11)' dspace.log.2018-02-07 | grep -o -E 'ip_addr=[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}' | sort -n | uniq -c | sort -n | tail -n 20
34 ip_addr=46.229.168.67
34 ip_addr=46.229.168.73
37 ip_addr=46.229.168.76
40 ip_addr=34.232.65.41
41 ip_addr=46.229.168.71
44 ip_addr=197.210.168.174
55 ip_addr=181.137.2.214
55 ip_addr=213.55.99.121
58 ip_addr=46.229.168.65
64 ip_addr=66.249.66.91
67 ip_addr=66.249.66.90
71 ip_addr=207.46.13.54
78 ip_addr=130.82.1.40
104 ip_addr=40.77.167.36
151 ip_addr=68.180.228.157
174 ip_addr=207.46.13.135
194 ip_addr=54.83.138.123
198 ip_addr=40.77.167.62
210 ip_addr=207.46.13.71
214 ip_addr=104.196.152.243
```
- These IPs made thousands of sessions today:
```
$ grep 104.196.152.243 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
530
$ grep 207.46.13.71 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
859
$ grep 40.77.167.62 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
610
$ grep 54.83.138.123 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
8
$ grep 207.46.13.135 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
826
$ grep 68.180.228.157 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
727
$ grep 40.77.167.36 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
181
$ grep 130.82.1.40 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
24
$ grep 207.46.13.54 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
166
$ grep 46.229.168 dspace.log.2018-02-07 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
992
```
- Let's investigate who these IPs belong to:
- 104.196.152.243 is CIAT, which is already marked as a bot via nginx!
- 207.46.13.71 is Bing, which is already marked as a bot in Tomcat's Crawler Session Manager Valve!
- 40.77.167.62 is Bing, which is already marked as a bot in Tomcat's Crawler Session Manager Valve!
- 207.46.13.135 is Bing, which is already marked as a bot in Tomcat's Crawler Session Manager Valve!
- 68.180.228.157 is Yahoo, which is already marked as a bot in Tomcat's Crawler Session Manager Valve!
- 40.77.167.36 is Bing, which is already marked as a bot in Tomcat's Crawler Session Manager Valve!
- 207.46.13.54 is Bing, which is already marked as a bot in Tomcat's Crawler Session Manager Valve!
- 46.229.168.x is Semrush, which is already marked as a bot in Tomcat's Crawler Session Manager Valve!
- Nice, so these are all known bots that are already crammed into one session by Tomcat's Crawler Session Manager Valve.
- What in the actual fuck, why is our load doing this? It's gotta be something fucked up with the database pool being "busy" but everything is fucking idle
- One that I should probably add in nginx is 54.83.138.123, which is apparently the following user agent:
```
BUbiNG (+http://law.di.unimi.it/BUbiNG.html)
```
- This one makes two thousand requests per day or so recently:
```
# grep -c BUbiNG /var/log/nginx/access.log /var/log/nginx/access.log.1
/var/log/nginx/access.log:1925
/var/log/nginx/access.log.1:2029
```
- And they have 30 IPs, so fuck that shit I'm going to add them to the Tomcat Crawler Session Manager Valve nowwww
- Lots of discussions on the dspace-tech mailing list over the last few years about leaky transactions being a known problem with DSpace
- Helix84 recommends restarting PostgreSQL instead of Tomcat because it restarts quicker
- This is how the connections looked when it crashed this afternoon:
```
$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
290 dspaceWeb
```
- This is how it is right now:
```
$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
5 dspaceWeb
```
- So is this just some fucked up XMLUI database leaking?
- I notice there is an issue (that I've probably noticed before) on the Jira tracker about this that was fixed in DSpace 5.7: https://jira.duraspace.org/browse/DS-3551
- I seriously doubt this leaking shit is fixed for sure, but I'm gonna cherry-pick all those commits and try them on DSpace Test and probably even CGSpace because I'm fed up with this shit
Update notes
2018-02-07 23:56:53 +01:00
- I cherry-picked all the commits for DS-3551 but it won't build on our current DSpace 5.5!
Update notes for 2018-02-07
2018-02-08 00:08:36 +01:00
- I sent a message to the dspace-tech mailing list asking why DSpace thinks these connections are busy when PostgreSQL says they are idle
Add notes for 2018-02-11
2018-02-11 09:01:13 +01:00
## 2018-02-11
- Magdalena from CCAFS emailed to ask why one of their items has such a weird thumbnail: [10568/90735](https://cgspace.cgiar.org/handle/10568/90735)
![Weird thumbnail](/cgspace-notes/2018/02/CCAFS_WP_223.pdf.jpg)
- I downloaded the PDF and manually generated a thumbnail with ImageMagick and it looked better:
```
$ convert CCAFS_WP_223.pdf\[0\] -profile /usr/local/share/ghostscript/9.22/iccprofiles/default_cmyk.icc -thumbnail 600x600 -flatten -profile /usr/local/share/ghostscript/9.22/iccprofiles/default_rgb.icc CCAFS_WP_223.jpg
```
![Manual thumbnail](/cgspace-notes/2018/02/CCAFS_WP_223.jpg)
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