+++ date = "2016-07-01T10:53:00+03:00" author = "Alan Orth" title = "July, 2016" tags = ["Notes"] +++ ## 2016-07-01 - Add `dc.description.sponsorship` to Discovery sidebar facets and make investors clickable in item view ([#232](https://github.com/ilri/DSpace/issues/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](https://jira.duraspace.org/browse/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` and `authority` 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](https://jira.duraspace.org/browse/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](https://httpoxy.org) 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 ([#255](https://github.com/ilri/DSpace/pull/255) - It 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](https://github.com/ilri/DSpace/pull/256)) ![About page](/cgspace-notes/2016/07/cgspace-about-page.png) - 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](https://github.com/ilri/DSpace/issues/257))