January, 2021

Sun Jan 03, 2021 in Notes

2021-01-03

Peter notified me that some filters on AReS were broken again
- It’s the same issue with the field names getting .keyword appended to the end that I already filed an issue on OpenRXV about last month
- I fixed the broken filters (careful to not edit any others, lest they break too!)
Fix an issue with start page number for the DSpace REST API and statistics API in OpenRXV
- The start page had been “1” in the UI, but in the backend they were doing some gymnastics to adjust to the zero-based offset/limit/page of the DSpace REST API and the statistics API
- I adjusted it to default to 0 and added a note to the admin screen
- I realized that this issue was actually causing the first page of 100 statistics to be missing…
- For example, this item has 51 views on CGSpace, but 0 on AReS

Start a re-index on AReS
- First delete the old Elasticsearch temp index:

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

Then, the next morning when it’s done, check the results of the harvesting, backup the current openrxv-items index, and clone the openrxv-items-temp index to openrxv-items:

$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
{
  "count" : 100278,
  "_shards" : {
    "total" : 1,
    "successful" : 1,
    "skipped" : 0,
    "failed" : 0
  }
}
$ 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-2021-01-04
$ 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
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
$ curl -XDELETE 'http://localhost:9200/openrxv-items-2021-01-04'

2021-01-04

There is one item that appears twice in AReS: 10568/66839
- If I use the Handle filter I see it twice… whereas other items don’t appear twice
- I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/67
Help Peter troubleshoot an issue with Altmetric badges on AReS
- He generated a report of our repository from Altmetric and noticed that many were missing scores despite having scores on CGSpace item pages
- AReS harvest Altmetric scores using the Handle prefix (10568) in batch, while CGSpace uses the DOI if it is found, and falls back to using the Handle
- I think it’s due to the fact that some items were never tweeted, so Altmetric never made the link between the DOI and the Handle
- I did some tweets of five items and within an hour or so the DOI API link registers the associated Handle, and within an hour or so the Handle API link is live with the same score

2021-01-05

A user sent me feedback about the dspace-statistics-api
- He noticed that the indexer fails if there are unmigrated legacy records in Solr
- I added a UUID filter to the queries in the indexer
I generated a CSV of titles and Handles for 2019 and 2020 items for Peter to Tweet
- We need to make sure that Altmetric has linked them all with their DOIs
- I wrote a quick and dirty script called doi-to-handle.py to read the DOIs from a text file, query the database, and save the handles and titles to a CSV
Help Udana export IWMI records from AReS
- He wanted me to give him CSV export permissions on CGSpace, but I told him that this requires super admin so I’m not comfortable with it
Import one item to CGSpace for Peter

2021-01-07

Import twenty CABI book chapters for Abenet
Udana and some editors from IWMI are still having problems editing metadata during the workflow step
- It is the same issue Peter reported last month, that values he edits are not saved when the item gets archived
- I added myself the the edit and approval steps of the collection on DSpace Test and asked Udana to submit an item there for me to test
Atmire got back to me about the duplicate data in Solr
- They want to arrange a time for us to do the stats processing so they can monitor it
- I proposed that I set everything up with a fresh Solr snapshot from CGSpace and then let them start the stats process

2021-01-10

Dominique from IWMI asked about API access to the IWMI collections
- A partner of theirs called AMCOW is interested in harvesting their publications
- I told her that they can use the REST API or OAI to get them from the IWMI Journal Articles collection:
  - CGSpace REST API: https://cgspace.cgiar.org/rest/collections/c2618391-184e-4091-8a93-280fdf01238b/items
  - CGSpace OAI API: https://cgspace.cgiar.org/oai/request?verb=ListRecords&metadataPrefix=oai_dc&set=col_10568_36185
Udana submitted an item to the collection on DSpace Test that I discussed last week
- I was able to take the task, add a new AGROVOC subject, approve the task, and commit it to archive
- The final item had my new AGROVOC subject, so I don’t see the issue
- Perhaps the issue only occurs when we replace an existing field? Or only on IWMI fields? I don’t know…
- Also there is this warning that occurs in the DSpace log during editing (and many other operations):

2021-01-10 10:03:27,692 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=1e8fb96c-b994-4fe2-8f0c-0a98ab138be0, ObjectType=(Unknown), ObjectID=null, TimeStamp=1610269383279, dispatcher=1544803905, detail=[null], transactionID="TX35636856957739531161091194485578658698")

I filed a bug on Atmire’s issue tracker
Peter asked me to move the CGIAR Gender Platform community to the top level of CGSpace, but I get an error when I use the community-filiator command:

$ dspace community-filiator --remove --parent=10568/66598 --child=10568/106605
Loading @mire database changes for module MQM
Changes have been processed
Exception: null
java.lang.UnsupportedOperationException
        at java.util.AbstractList.remove(AbstractList.java:161)
        at java.util.AbstractList$Itr.remove(AbstractList.java:374)
        at java.util.AbstractCollection.remove(AbstractCollection.java:293)
        at org.dspace.administer.CommunityFiliator.defiliate(CommunityFiliator.java:264)
        at org.dspace.administer.CommunityFiliator.main(CommunityFiliator.java:164)
        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 is apparently a bug in DSpace 6.x that makes community-filiator not work
- There is a patch for the as-of-yet unreleased DSpace 6.4 so I will try that
Udana had asked about exporting IWMI’s community on CGSpace, but we don’t want to give him super admin permissions to do that
- I suggested that he use AReS, but there are some fields missing because we don’t harvest them all
- I added a few more fields to the configuration and will start a fresh harvest.
Start a re-index on AReS
- First delete the old Elasticsearch temp index:

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