February, 2021

Mon Feb 01, 2021 in Notes

2021-02-01

Abenet said that CIP found more duplicate records in their export from AReS
- I re-opened the issue on OpenRXV where we had previously noticed this
- The shared link where the duplicates are is here: https://cgspace.cgiar.org/explorer/shared/heEOz3YBnXdK69bR2ra6
I had a call with CodeObia to discuss the work on OpenRXV
Check the results of the AReS harvesting from last night:

$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
{
  "count" : 100875,
  "_shards" : {
    "total" : 1,
    "successful" : 1,
    "skipped" : 0,
    "failed" : 0
  }
}

Set the current items index to read only and make a backup:

$ curl -X PUT "localhost:9200/openrxv-items/_settings" -H 'Content-Type: application/json' -d'
{"settings": {"index.blocks.write":true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2021-02-01

Delete the current items index and clone the temp one to it:

$ curl -XDELETE 'http://localhost:9200/openrxv-items'
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items

Then delete the temp and backup:

$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'       
{"acknowledged":true}%                                                                                                               
$ curl -XDELETE 'http://localhost:9200/openrxv-items-2021-02-01'

Meeting with Peter and Abenet about CGSpace goals and progress
Test submission to DSpace via REST API to see if Abenet can fix / reject it (submit workflow?)
Get Peter a list of users who have submitted or approved on DSpace everrrrrrr, so he can remove some
Ask MEL for a dump of their types to reconcile with ours and CG Core
Need to tag ILRI collection with license!! For pre-2010 use “Other” unless a license is already there; 2010-2020 do the ilri content in batches (2010-2015: CC-BY-NC-SA; 2016-onwards: CC-BY);
- ONLY if ILRI / International Livestock Research Institute is the publisher, no journal articles, no book chapters…
I tried to export the ILRI community from CGSpace but I got an error:

$ dspace metadata-export -i 10568/1 -f /tmp/2021-02-01-ILRI.csv
Loading @mire database changes for module MQM
Changes have been processed
Exporting community 'International Livestock Research Institute (ILRI)' (10568/1)
           Exception: null
java.lang.NullPointerException
        at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:212)
        at com.google.common.collect.Iterators.concat(Iterators.java:464)
        at org.dspace.app.bulkedit.MetadataExport.addItemsToResult(MetadataExport.java:136)
        at org.dspace.app.bulkedit.MetadataExport.buildFromCommunity(MetadataExport.java:125)
        at org.dspace.app.bulkedit.MetadataExport.<init>(MetadataExport.java:77)
        at org.dspace.app.bulkedit.MetadataExport.main(MetadataExport.java:282)
        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)

I imported the production database to my local development environment and I get the same error… WTF is this?
- I was able to export another smaller community
- I filed an issue with Atmire to see if it is likely something of theirs, or if I need to ask on the dspace-tech mailing list
CodeObia sent a pull request with fixes for several issues we highlighted in OpenRXV
- I deployed the fixes on production, as they only affect minor parts of the frontend, and two of the four are working
- I sent feedback to CodeObia

2021-02-02

Communicate more with CodeObia about some fixes for OpenRXV
Maria Garruccio sent me some new ORCID iDs for Bioversity authors, as well as a correction for Stefan Burkart’s iD
I saved the new ones to a text file, combined them with the others, extracted the ORCID iDs themselves, and updated the names using resolve-orcids.py:
Then for the rest, I saved them to a text file, combined them with the others, extracted the ORCID iDs themselves, and updated the names using resolve-orcids.py:

$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity-orcid-ids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2021-02-02-combined-orcids.txt
$ ./ilri/resolve-orcids.py -i /tmp/2021-02-02-combined-orcids.txt -o /tmp/2021-02-02-combined-orcid-names.txt

I sorted the names and added the XML formatting in vim, then ran it through tidy:

$ tidy -xml -utf8 -m -iq -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml

Then I added all the changed names plus Stefan’s incorrect ones to a CSV and processed them with fix-metadata-values.py:

$ cat 2021-02-02-fix-orcid-ids.csv 
cg.creator.id,correct
Burkart Stefan: 0000-0001-5297-2184,Stefan Burkart: 0000-0001-5297-2184
Burkart Stefan: 0000-0002-7558-9177,Stefan Burkart: 0000-0001-5297-2184
Stefan  Burkart: 0000-0001-5297-2184,Stefan Burkart: 0000-0001-5297-2184
Stefan Burkart: 0000-0002-7558-9177,Stefan Burkart: 0000-0001-5297-2184
Adina Chain Guadarrama: 0000-0002-6944-2064,Adina Chain-Guadarrama: 0000-0002-6944-2064
Bedru: 0000-0002-7344-5743,Bedru B. Balana: 0000-0002-7344-5743
Leigh Winowiecki: 0000-0001-5572-1284,Leigh Ann Winowiecki: 0000-0001-5572-1284
Sander J. Zwart: 0000-0002-5091-1801,Sander Zwart: 0000-0002-5091-1801
saul lozano-fuentes: 0000-0003-1517-6853,Saul Lozano: 0000-0003-1517-6853
$ ./ilri/fix-metadata-values.py -i 2021-02-02-fix-orcid-ids.csv -db dspace63 -u dspace -p 'fuuu' -f cg.creator.id -t 'correct' -m 240

I also looked up which of these new authors might have existing items that are missing ORCID iDs
I had to port my add-orcid-identifiers-csv.py to DSpace 6 UUIDs and I think it’s working but I want to do a few more tests because it uses a sequence for the metadata_value_id

2021-02-03

Tag forty-three items from Bioversity’s new authors with ORCID iDs using add-orcid-identifiers-csv.py:

$ cat /tmp/2021-02-02-add-orcid-ids.csv
dc.contributor.author,cg.creator.id
"Nchanji, E.",Eileen Bogweh Nchanji: 0000-0002-6859-0962
"Nchanji, Eileen",Eileen Bogweh Nchanji: 0000-0002-6859-0962
"Nchanji, Eileen Bogweh",Eileen Bogweh Nchanji: 0000-0002-6859-0962
"Machida, Lewis",Lewis Machida: 0000-0002-0012-3997
"Mockshell, Jonathan",Jonathan Mockshell: 0000-0003-1990-6657"
"Aubert, C.",Celine Aubert: 0000-0001-6284-4821
"Aubert, Céline",Celine Aubert: 0000-0001-6284-4821
"Devare, M.",Medha Devare: 0000-0003-0041-4812
"Devare, Medha",Medha Devare: 0000-0003-0041-4812
"Benites-Alfaro, O.E.",Omar E. Benites-Alfaro: 0000-0002-6852-9598
"Benites-Alfaro, Omar Eduardo",Omar E. Benites-Alfaro: 0000-0002-6852-9598
"Johnson, Vincent",VINCENT JOHNSON: 0000-0001-7874-178X
"Lesueur, Didier",didier lesueur: 0000-0002-6694-0869
$ ./ilri/add-orcid-identifiers-csv.py -i /tmp/2021-02-02-add-orcid-ids.csv -db dspace -u dspace -p 'fuuu' -d

I’m working on the CGSpace accession for Karl Rich’s Viet Nam Pig Model 2018 and I noticed his ORCID iD is missing from CGSpace
- I added it and tagged 141 items of his with the iD
I uploaded a metadata-only accession for the impact of ILRI book by John McIntire and Delia Grace to CGSpace
- The source code itself is here: https://github.com/ilri/impact-book
A little bit more work on CG Core v2

2021-02-04

Re-sync CGSpace database and Solr to DSpace Test to start a public test of CG Core v2
- Afterwards I updated Discovery and OAI:

$ time chrt -b 0 dspace index-discovery -b
$ dspace oai import -c

Attend Accenture meeting for repository managers
- Not clear what the SMO wants to get out of us
Enrico asked for some notes about our work on AReS in 2020 for CRP Livestock reporting
- Abenet and I came up with the following:

In 2020 we funded the third phase of development on the OpenRXV platform that powers AReS. This phase focused mainly on improving the search filtering, graphical visualizations, and reporting capabilities. It is now possible to create custom reports in Excel, Word, and PDF formats using a templating system. We also concentrated on making the vanilla OpenRXV platform easier to deploy and administer in hopes that other organizations would begin using it. Lastly, we identified and fixed a handful of bugs in the system. All development takes place publicly on GitHub: https://github.com/ilri/OpenRXV.

In the last quarter of 2020, ILRI conducted a briefing for nearly 100 scientists and communications staff on how to use ARes as a visualization tool for repository outputs and as a reporting tool (https://hdl.handle.net/10568/110527). Staff will begin using AReS to generate lists of their outputs to upload in the performance evaluation system to assist in their performance evaluation. The list of publications they will upload from AReS to Performax will indicate the open access status of each publication to help start discussion why some outputs are not open access given the open access policies of the CGIAR.

Call Moayad to discuss OpenRXV development
- We talked about the “reporting period” (date-based statistics) and some of the issues Abdullah is working on on GitHub
- I suggested that we offer the date-range statistics in a modal dialog with other sorting and grouping options during report generation
Peter sent me the cleaned up series that I had originally sent him in 2020-10
- I quickly applied all the deletions on CGSpace:

$ ./ilri/delete-metadata-values.py -i /tmp/2020-10-28-Series-PB.csv -db dspace -u dspace -p 'fuuu' -f dc.relation.ispartofseries -m 43

The corrected versions have a lot of encoding issues so I asked Peter to give me the correct ones so I can search/replace them:
- CIAT PublicaÃ§ao
- CIAT PublicaciÃ³n
- CIAT SÃ©rie
- CIAT SÃ©ries
- ColecciÃ³n investigaciÃ³n y desarrollo
- CTA Guias prÃ¡ticos
- CTA Guias tÃ©cnicas
- Curso de adiestramiento en producciÃ³n y utilizaciÃ³n de pastos tropicales
- Folheto TÃ©cnico
- ILRI Nota Informativa de InvestigaÃ§Ã£o
- Influencia de los actores sociales en AmÃ©rica Central
- Institutionalization of quality assurance mechanism and dissemination of top quality commercial products to increase crop yields and improve food security of smallholder farmers in sub-Saharan Africa â€“ COMPRO-II
- Manuel pour les Banques de GÃ¨nes;1
- SistematizaciÃ³n de experiencias Proyecto ACORDAR
- StrÃ¼ngmann Forum
- UnitÃ© de Recherche
I ended up using python-ftfy to fix those very easily, then replaced them in the CSV
Then I trimmed whitespace at the beginning, end, and around the “;”, and applied the 1,600 fixes using fix-metadata-values.py:

$ ./ilri/fix-metadata-values.py -i /tmp/2020-10-28-Series-PB.csv -db dspace -u dspace -p 'fuuu' -f dc.relation.ispartofseries -t 'correct' -m 43

Help Peter debug an issue with one of Alan Duncan’s new FEAST Data reports on CGSpace
- For some reason the default policy for the item was “COLLECTION_492_DEFAULT_READ” group, which had zero members
- I changed them all to Anonymous and the item was accessible

2021-02-07

Run system updates on CGSpace (linode18), deploy latest 6_x-prod branch, and reboot the server
After the server came back up I started a full Discovery re-indexing:

$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b

real    247m30.850s
user    160m36.657s
sys     2m26.050s

Regarding the CG Core v2 migration, Fabio wrote to tell me that he is not using CGSpace directly, instead harvesting via GARDIAN
- He gave me the contact of Sotiris Konstantinidis, who is the CTO at SCIO Systems and works on the GARDIAN platform
Delete the old Elasticsearch temp index to prepare for starting an AReS re-harvest:

$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
# start indexing in AReS