CGSpace 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
• 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

• Run all system updates and reboot DSpace Test
• Wow, I packaged up the jmx_dspace_sessions stuff in the Ansible infrastructure scripts 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

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
• 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

real    96m39.823s
user    14m10.975s
sys     2m29.088s

• 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:

# time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Jan/2018"
3126109

real    0m23.839s
user    0m27.225s
sys     0m1.905s

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

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 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 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
• I deployed the changes on DSpace Test only for now, so I will monitor and make them on CGSpace later this week