+
+ 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
+
+
+
+
+
+
+
+