CGSpace Notes

Documenting day-to-day work on the CGSpace repository.

November, 2017

by Alan Orth in  

2017-11-01

  • The CORE developers responded to say they are looking into their bot not respecting our robots.txt

2017-11-02

  • Today there have been no hits by CORE and no alerts from Linode (coincidence?)
# grep -c "CORE" /var/log/nginx/access.log
0
  • Generate list of authors on CGSpace for Peter to go through and correct:
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.csv with csv;
COPY 54701

  • Abenet asked if it would be possible to generate a report of items in Listing and Reports that had “International Fund for Agricultural Development” as the only investor
  • I opened a ticket with Atmire to ask if this was possible: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=540
  • Work on making the thumbnails in the item view clickable
  • Basically, once you read the METS XML for an item it becomes easy to trace the structure to find the bitstream link
//mets:fileSec/mets:fileGrp[@USE='CONTENT']/mets:file/mets:FLocat[@LOCTYPE='URL']/@xlink:href
  • METS XML is available for all items with this pattern: /metadata/handle/10568/95947/mets.xml
  • I whipped up a quick hack to print a clickable link with this URL on the thumbnail but it needs to check a few corner cases, like when there is a thumbnail but no content bitstream!
  • Help proof fifty-three CIAT records for Sisay: https://dspacetest.cgiar.org/handle/10568/95895
  • A handful of issues with cg.place using format like “Lima, PE” instead of “Lima, Peru”
  • Also, some dates like with completely invalid format like “2010- 06” and “2011-3-28”
  • I also collapsed some consecutive whitespace on a handful of fields

2017-11-03

  • Atmire got back to us to say that they estimate it will take two days of labor to implement the change to Listings and Reports
  • I said I’d ask Abenet if she wants that feature

2017-11-04

  • I finished looking through Sisay’s CIAT records for the “Alianzas de Aprendizaje” data
  • I corrected about half of the authors to standardize them
  • Linode emailed this morning to say that the CPU usage was high again, this time at 6:14AM
  • It’s the first time in a few days that this has happened
  • I had a look to see what was going on, but it isn’t the CORE bot:
# awk '{print $1}' /var/log/nginx/access.log | sort -n | uniq -c | sort -h | tail
    306 68.180.229.31
    323 61.148.244.116
    414 66.249.66.91
    507 40.77.167.16
    618 157.55.39.161
    652 207.46.13.103
    666 157.55.39.254
   1173 104.196.152.243
   1737 66.249.66.90
  23101 138.201.52.218
  • 138.201.52.218 is from some Hetzner server, and I see it making 40,000 requests yesterday too, but none before that:
# zgrep -c 138.201.52.218 /var/log/nginx/access.log*
/var/log/nginx/access.log:24403
/var/log/nginx/access.log.1:45958
/var/log/nginx/access.log.2.gz:0
/var/log/nginx/access.log.3.gz:0
/var/log/nginx/access.log.4.gz:0
/var/log/nginx/access.log.5.gz:0
/var/log/nginx/access.log.6.gz:0
  • It’s clearly a bot as it’s making tens of thousands of requests, but it’s using a “normal” user agent:
Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2227.0 Safari/537.36
  • For now I don’t know what this user is!

2017-11-05

  • Peter asked if I could fix the appearance of “International Livestock Research Institute” in the author lookup during item submission
  • It looks to be just an issue with the user interface expecting authors to have both a first and last name:

Author lookup Add author

  • But in the database the authors are correct (none with weird , / characters):
dspace=# select distinct text_value, authority, confidence from metadatavalue value where resource_type_id=2 and metadata_field_id=3 and text_value like 'International Livestock Research Institute%';
                 text_value                 |              authority               | confidence 
--------------------------------------------+--------------------------------------+------------
 International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c |          0
 International Livestock Research Institute | f4db1627-47cd-4699-b394-bab7eba6dadc |          0
 International Livestock Research Institute |                                      |         -1
 International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c |        600
 International Livestock Research Institute | f4db1627-47cd-4699-b394-bab7eba6dadc |         -1
 International Livestock Research Institute |                                      |        600
 International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c |         -1
 International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c |        500
(8 rows)
  • So I’m not sure if this is just a graphical glitch or if editors have to edit this metadata field prior to approval
  • Looking at monitoring Tomcat’s JVM heap with Prometheus, it looks like we need to use JMX + jmx_exporter
  • This guide shows how to enable JMX in Tomcat by modifying CATALINA_OPTS
  • I was able to successfully connect to my local Tomcat with jconsole!