cgspace-notes/content/posts/2020-09.md

---
title: "September, 2020"
date: 2020-09-02T15:35:54+03:00
author: "Alan Orth"
categories: ["Notes"]
---

## 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 a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/39
- I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40

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- 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](https://wiki.lyrasis.org/display/DSDOC6x/Authentication+Plugins#AuthenticationPlugins-LDAPAuthentication) 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](https://github.com/ilri/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](https://dspacetest.cgiar.org/handle/10568/108357) 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

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