July, 2016
2016-07-01
- Add
dc.description.sponsorship
to Discovery sidebar facets and make investors clickable in item view (#232) I think this query should find and replace all authors that have “,” at the end of their names:
dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$'; UPDATE 95 dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$'; text_value ------------ (0 rows)
In this case the select query was showing 95 results before the update
2016-07-02
- Comment on DSpace Jira ticket about author lookup search text (DS-2329)
2016-07-04
- Seems the database’s author authority values mean nothing without the
authority
Solr core from the host where they were created!
2016-07-05
- Amend
backup-solr.sh
script so it backs up the entire Solr folder - We really only need
statistics
andauthority
but meh Fix metadata for species on DSpace Test:
$ ./fix-metadata-values.py -i /tmp/Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 94 -d dspacetest -u dspacetest -p 'fuuu'
Will run later on CGSpace
A user is still having problems with Sherpa/Romeo causing crashes during the submission process when the journal is “ungraded”
I tested the patch for DS-2740 that I had found last month and it seems to work
I will merge it to
5_x-prod
2016-07-06
Delete 23 blank metadata values from CGSpace:
cgspace=# delete from metadatavalue where resource_type_id=2 and text_value=''; DELETE 23
Complete phase three of metadata migration, for the following fields:
- dc.title.jtitle → dc.source
- dc.crsubject.crpsubject → cg.contributor.crp
- dc.contributor.affiliation → cg.contributor.affiliation
- dc.Species → cg.species
- dc.srplace.subregion → cg.coverage.subregion
- dc.contributor.corporate → dc.contributor.author
- dc.identifier.url → cg.identifier.url
- dc.identifier.doi → cg.identifier.doi
- dc.identifier.googleurl → cg.identifier.googleurl
- dc.identifier.dataurl → cg.identifier.dataurl
Also, run fixes and deletes for species and author affiliations (over 1000 corrections!)
$ ./fix-metadata-values.py -i Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 212 -d dspace -u dspace -p 'fuuu' $ ./fix-metadata-values.py -i Affiliations-Fix-1045-Peter-Abenet.csv -f dc.contributor.affiliation -t Correct -m 211 -d dspace -u dspace -p 'fuuu' $ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Delete-Peter-Abenet.csv -m 211 -u dspace -d dspace -p 'fuuu'
I then ran all server updates and rebooted the server
2016-07-11
Doing some author cleanups from Peter and Abenet:
$ ./fix-metadata-values.py -i /tmp/Authors-Fix-205-UTF8.csv -f dc.contributor.author -t correct -m 3 -d dspacetest -u dspacetest -p fuuu $ ./delete-metadata-values.py -f dc.contributor.author -i /tmp/Authors-Delete-UTF8.csv -m 3 -u dspacetest -d dspacetest -p fuuu
2016-07-13
- Run the author cleanups on CGSpace and start a full Discovery re-index
2016-07-14
- Test LDAP settings for new root LDAP
- Seems to work when binding as a top-level user
2016-07-18
- Adjust identifiers in XMLUI item display to be more prominent
- Add species and breed to the XMLUI item display
CGSpace crashed late at night and the DSpace logs were showing:
2016-07-18 20:26:30,941 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error - org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object ...
I suspect it’s someone hitting REST too much:
# awk '{print $1}' /var/log/nginx/rest.log | sort -n | uniq -c | sort -h | tail -n 3 710 66.249.78.38 1781 181.118.144.29 24904 70.32.99.142
I just blocked access to
/rest
for that last IP for now:# log rest requests location /rest { access_log /var/log/nginx/rest.log; proxy_pass http://127.0.0.1:8443; deny 70.32.99.142; }
2016-07-21
- Mitigate the HTTPoxy vulnerability for Tomcat etc in nginx: https://github.com/ilri/rmg-ansible-public/pull/38
- Unblock 70.32.99.142 from
/rest
as it has been blocked for a few days
2016-07-22
- Help Paola from CCAFS with thumbnails for batch uploads
- She has been struggling to get the dimensions right, and manually enlarging smaller thumbnails, renaming PNGs to JPG, etc
- Altmetric reports having an issue with some of our authors being doubled…
- This is related to authority and confidence!
- We might need to use
index.authority.ignore-prefered=true
to tell the Discovery index to prefer the variation that exists in the metadatavalue rather than what it finds in the authority cache. Trying these on DSpace Test after a discussion by Daniel Scharon on the dspace-tech mailing list:
index.authority.ignore-prefered.dc.contributor.author=true index.authority.ignore-variants.dc.contributor.author=false
After reindexing I don’t see any change in Discovery’s display of authors, and still have entries like:
Grace, D. (464) Grace, D. (62)
I asked for clarification of the following options on the DSpace mailing list:
index.authority.ignore index.authority.ignore-prefered index.authority.ignore-variants
In the mean time, I will try these on DSpace Test (plus a reindex):
index.authority.ignore=true index.authority.ignore-prefered=true index.authority.ignore-variants=true
Enabled usage of
X-Forwarded-For
in DSpace admin control panel (#255It was misconfigured and disabled, but already working for some reason sigh
… no luck. Trying with just:
index.authority.ignore=true
After re-indexing and clearing the XMLUI cache nothing has changed
2016-07-25
Trying a few more settings (plus reindex) for Discovery on DSpace Test:
index.authority.ignore-prefered.dc.contributor.author=true index.authority.ignore-variants=true
Run all OS updates and reboot DSpace Test server
No changes to Discovery after reindexing… hmm.
Integrate and massively clean up About page (#256)
The DSpace source code mentions the configuration key
discovery.index.authority.ignore-prefered.*
(with prefix of discovery, despite the docs saying otherwise), so I’m trying the following on DSpace Test:discovery.index.authority.ignore-prefered.dc.contributor.author=true discovery.index.authority.ignore-variants=true
Still no change!
Deploy species, breed, and identifier changes to CGSpace, as well as About page
Run Linode RAM upgrade (8→12GB)
Re-sync DSpace Test with CGSpace
I noticed that our backup scripts don’t send Solr cores to S3 so I amended the script
2016-07-31
- Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by
- Also change “Subjects” to “AGROVOC keywords” in Discovery sidebar/search and Browse by (#257)