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Alan Orth
d3d413c991
The theme used to have a <base> tag, which tells the browser which base to use for relative URLs, but this was actually a buggy and incorrect theme behavior, so we need to update our links. $ sed -i 's/(\(201[567]\)/(\/cgspace-notes\/\1/' content/post/*.md
213 lines
7.4 KiB
Markdown
213 lines
7.4 KiB
Markdown
+++
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date = "2016-07-01T10:53:00+03:00"
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author = "Alan Orth"
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title = "July, 2016"
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tags = ["Notes"]
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+++
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## 2016-07-01
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- Add `dc.description.sponsorship` to Discovery sidebar facets and make investors clickable in item view ([#232](https://github.com/ilri/DSpace/issues/232))
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- I think this query should find and replace all authors that have "," at the end of their names:
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```
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dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
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UPDATE 95
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dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
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text_value
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------------
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(0 rows)
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```
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- In this case the select query was showing 95 results before the update
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<!--more-->
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## 2016-07-02
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- Comment on DSpace Jira ticket about author lookup search text ([DS-2329](https://jira.duraspace.org/browse/DS-2329))
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## 2016-07-04
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- Seems the database's author authority values mean nothing without the `authority` Solr core from the host where they were created!
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## 2016-07-05
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- Amend `backup-solr.sh` script so it backs up the entire Solr folder
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- We *really* only need `statistics` and `authority` but meh
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- Fix metadata for species on DSpace Test:
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```
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$ ./fix-metadata-values.py -i /tmp/Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 94 -d dspacetest -u dspacetest -p 'fuuu'
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```
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- Will run later on CGSpace
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- A user is still having problems with Sherpa/Romeo causing crashes during the submission process when the journal is "ungraded"
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- 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
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- I will merge it to `5_x-prod`
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## 2016-07-06
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- Delete 23 blank metadata values from CGSpace:
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```
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cgspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
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DELETE 23
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```
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- Complete phase three of metadata migration, for the following fields:
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- dc.title.jtitle → dc.source
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- dc.crsubject.crpsubject → cg.contributor.crp
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- dc.contributor.affiliation → cg.contributor.affiliation
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- dc.Species → cg.species
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- dc.srplace.subregion → cg.coverage.subregion
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- dc.contributor.corporate → dc.contributor.author
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- dc.identifier.url → cg.identifier.url
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- dc.identifier.doi → cg.identifier.doi
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- dc.identifier.googleurl → cg.identifier.googleurl
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- dc.identifier.dataurl → cg.identifier.dataurl
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- Also, run fixes and deletes for species and author affiliations (over 1000 corrections!)
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```
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$ ./fix-metadata-values.py -i Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 212 -d dspace -u dspace -p 'fuuu'
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$ ./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'
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$ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Delete-Peter-Abenet.csv -m 211 -u dspace -d dspace -p 'fuuu'
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```
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- I then ran all server updates and rebooted the server
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## 2016-07-11
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- Doing some author cleanups from Peter and Abenet:
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```
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$ ./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
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$ ./delete-metadata-values.py -f dc.contributor.author -i /tmp/Authors-Delete-UTF8.csv -m 3 -u dspacetest -d dspacetest -p fuuu
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```
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## 2016-07-13
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- Run the author cleanups on CGSpace and start a full Discovery re-index
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## 2016-07-14
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- Test LDAP settings for new root LDAP
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- Seems to work when binding as a top-level user
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## 2016-07-18
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- Adjust identifiers in XMLUI item display to be more prominent
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- Add species and breed to the XMLUI item display
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- CGSpace crashed late at night and the DSpace logs were showing:
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```
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2016-07-18 20:26:30,941 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
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org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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...
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```
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- I suspect it's someone hitting REST too much:
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```
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# awk '{print $1}' /var/log/nginx/rest.log | sort -n | uniq -c | sort -h | tail -n 3
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710 66.249.78.38
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1781 181.118.144.29
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24904 70.32.99.142
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```
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- I just blocked access to `/rest` for that last IP for now:
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```
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# log rest requests
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location /rest {
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access_log /var/log/nginx/rest.log;
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proxy_pass http://127.0.0.1:8443;
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deny 70.32.99.142;
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}
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```
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## 2016-07-21
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- Mitigate the [HTTPoxy](https://httpoxy.org) vulnerability for Tomcat etc in nginx: https://github.com/ilri/rmg-ansible-public/pull/38
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- Unblock 70.32.99.142 from `/rest` as it has been blocked for a few days
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## 2016-07-22
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- Help Paola from CCAFS with thumbnails for batch uploads
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- She has been struggling to get the dimensions right, and manually enlarging smaller thumbnails, renaming PNGs to JPG, etc
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- Altmetric reports having an issue with some of our authors being doubled...
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- This is related to authority and confidence!
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- 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.
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- Trying these on DSpace Test after a discussion by Daniel Scharon on the dspace-tech mailing list:
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```
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index.authority.ignore-prefered.dc.contributor.author=true
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index.authority.ignore-variants.dc.contributor.author=false
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```
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- After reindexing I don't see any change in Discovery's display of authors, and still have entries like:
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```
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Grace, D. (464)
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Grace, D. (62)
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```
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- I asked for clarification of the following options on the DSpace mailing list:
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```
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index.authority.ignore
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index.authority.ignore-prefered
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index.authority.ignore-variants
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```
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- In the mean time, I will try these on DSpace Test (plus a reindex):
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```
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index.authority.ignore=true
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index.authority.ignore-prefered=true
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index.authority.ignore-variants=true
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```
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- Enabled usage of `X-Forwarded-For` in DSpace admin control panel ([#255](https://github.com/ilri/DSpace/pull/255)
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- It was misconfigured and disabled, but already working for some reason *sigh*
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- ... no luck. Trying with just:
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```
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index.authority.ignore=true
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```
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- After re-indexing and clearing the XMLUI cache nothing has changed
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## 2016-07-25
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- Trying a few more settings (plus reindex) for Discovery on DSpace Test:
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```
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index.authority.ignore-prefered.dc.contributor.author=true
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index.authority.ignore-variants=true
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```
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- Run all OS updates and reboot DSpace Test server
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- No changes to Discovery after reindexing... hmm.
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- Integrate and massively clean up About page ([#256](https://github.com/ilri/DSpace/pull/256))
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- 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:
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```
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discovery.index.authority.ignore-prefered.dc.contributor.author=true
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discovery.index.authority.ignore-variants=true
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```
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- Still no change!
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- Deploy species, breed, and identifier changes to CGSpace, as well as About page
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- Run Linode RAM upgrade (8→12GB)
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- Re-sync DSpace Test with CGSpace
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- I noticed that our backup scripts don't send Solr cores to S3 so I amended the script
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## 2016-07-31
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- Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by
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- Also change "Subjects" to "AGROVOC keywords" in Discovery sidebar/search and Browse by ([#257](https://github.com/ilri/DSpace/issues/257))
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