2020-09-02
- Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS
- The AReS Explorer hasn’t updated its index since 2020-08-22 when I last forced it
- I restarted it again now and told Moayad that the automatic indexing isn’t working
- Add
Alliance of Bioversity International and CIAT to affiliations on CGSpace
- Abenet told me that the general search text on AReS doesn’t get reset when you use the “Reset Filters” button
- I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40
- I ran the country code tagger on CGSpace:
$ time chrt -b 0 dspace curate -t countrycodetagger -i all -r - -l 500 -s object | tee /tmp/2020-09-02-countrycodetagger.log
...
real 2m10.516s
user 1m43.953s
sys 0m15.192s
$ grep -c added /tmp/2020-09-02-countrycodetagger.log
39
- I still need to create a cron job for this…
- Sisay and Abenet said they can’t log in with LDAP on DSpace Test (DSpace 6)
- I tried and I can’t either… but it is working on CGSpace
- The error on DSpace 6 is:
2020-09-02 12:03:10,666 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=A629116488DCC467E1EA2062A2E2EFD7:ip_addr=92.220.02.201:failed_login:no DN found for user aorth
- I tried to query LDAP directly using the application credentials with ldapsearch and it works:
$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b "dc=cgiarad,dc=org" -D "applicationaccount@cgiarad.org" -W "(sAMAccountName=me)"
- According to the DSpace 6 docs we need to escape commas in our LDAP parameters due to the new configuration system
- I added the commas and restarted DSpace (though technically we shouldn’t need to restart due to the new config system hot reloading configs)
- Run all system updates on DSpace Test (linode26) and reboot it
- After the restart LDAP login works…
2020-09-03
- Fix some erroneous “review status” fields that Abenet noticed on AReS
- I used my
fix-metadata-values.py and delete-metadata-values.py scripts with the following input files:
$ cat 2020-09-03-fix-review-status.csv
dc.description.version,correct
Externally Peer Reviewed,Peer Review
Peer Reviewed,Peer Review
Peer review,Peer Review
Peer reviewed,Peer Review
Peer-Reviewed,Peer Review
Peer-reviewed,Peer Review
peer Review,Peer Review
$ cat 2020-09-03-delete-review-status.csv
dc.description.version
Report
Formally Published
Poster
Unrefereed reprint
$ ./delete-metadata-values.py -i 2020-09-03-delete-review-status.csv -db dspace -u dspace -p 'fuuu' -f dc.description.version -m 68
$ ./fix-metadata-values.py -i 2020-09-03-fix-review-status.csv -db dspace -u dspace -p 'fuuu' -f dc.description.version -t 'correct' -m 68
- Start reviewing 95 items for IITA (20201stbatch)
- I used my csv-metadata-quality tool to check and fix some low-hanging fruit first
- This fixed a few unnecessary Unicode, excessive whitespace, invalid multi-value separator, and duplicate metadata values
- Then I looked at the data in OpenRefine and noticed some things:
- All issue dates use year only, but some have months in the citation so they could be more specific
- I normalized all the DOIs to use “https://doi.org” format
- I fixed a few AGROVOC subjects with a simple GREL:
value.replace("GRAINS","GRAIN").replace("SOILS","SOIL").replace("CORN","MAIZE")
- But there are a few more that are invalid that she will have to look at
- I uploaded the items to DSpace Test and it was apparently successful but I get these errors to the console:
Thu Sep 03 12:26:33 CEST 2020 | Query:containerItem:ea7a2648-180d-4fce-bdc5-c3aa2304fc58
Error while updating
java.lang.NullPointerException
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl$5.visit(SourceFile:1131)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.visitEachStatisticShard(SourceFile:212)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1104)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1093)
at org.dspace.statistics.StatisticsLoggingConsumer.consume(SourceFile:104)
at org.dspace.event.BasicDispatcher.consume(BasicDispatcher.java:177)
at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:123)
at org.dspace.core.Context.dispatchEvents(Context.java:455)
at org.dspace.core.Context.commit(Context.java:424)
at org.dspace.core.Context.complete(Context.java:380)
at org.dspace.app.bulkedit.MetadataImport.main(MetadataImport.java:1399)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
- There are more in the DSpace log so I will raise it with Atmire immediately