CGSpace Notes

Documenting day-to-day work on the CGSpace repository.

January, 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
  • 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
$ ./doi-to-handle.py -db dspace -u dspace -p 'fuuu' -i /tmp/dois.txt -o /tmp/out.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

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
    • I tested the patch on DSpace Test and it worked, so I will do the same on CGSpace tomorrow
  • 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
... after ten hours
$ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty'
{
  "count" : 100411,
  "_shards" : {
    "total" : 1,
    "successful" : 1,
    "skipped" : 0,
    "failed" : 0
  }
}
$ curl -X PUT "localhost:9200/openrxv-items-temp/_settings?pretty" -H 'Content-Type: application/json' -d'{"settings": {"index.blocks.write": true}}'
$ curl -XDELETE 'http://localhost:9200/openrxv-items'
$ curl -s -X POST http://localhost:9200/openrxv-items-temp/_clone/openrxv-items
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
  • Looking over the last month of Solr stats I see a familiar bot that should have been marked as a bot months ago:

Mozilla/5.0 (compatible; +centuryb.o.t9[at]gmail.com)

  • There are 51,961 hits from this bot on 64.62.202.71 and 64.62.202.73
    • Ah! Actually I added the bot pattern to the Tomcat Crawler Session Manager Valve, which mitigated the abuse of Tomcat sessions:
$ cat log/dspace.log.2020-12-2* | grep -E 'session_id=[A-Z0-9]{32}:ip_addr=64.62.202.71' | sort | uniq | wc -l
0
  • So now I should really add it to the DSpace spider agent list so it doesn’t create Solr hits
    • I added it to the “ilri” lists of spider agent patterns
  • I purged the existing hits using my check-spider-ip-hits.sh script:
$ ./check-spider-ip-hits.sh -d -f /tmp/ips -s http://localhost:8081/solr -s statistics -p

2021-01-11

  • The AReS indexing finished this morning and I moved the openrxv-items-temp core to openrxv-items (see above)
    • I sorted the explorer results by Altmetric attention score and I see a few new ones on the top so I think the recent tweeting of Handles by Peter and myself worked
  • I deployed the community-filiator fix on CGSpace and moved the Gender Platform community to the top level of CGSpace:
$ dspace community-filiator --remove --parent=10568/66598 --child=10568/106605

2021-01-12

  • IWMI is really pressuring us to have a periodic CSV export of their community
    • I decided to write a systemd timer to use dspace metadata-export every week, and made an nginx alias to make it available publicly
    • It is part of the Ansible infrastructure scripts that I use to provision the servers
  • I wrote to Atmire to tell them to try their CUA duplicates processor on DSpace Test whenever they get a chance this week
    • I verified that there were indeed duplicate metadata values in the userAgent_ngram and userAgent_search fields, even in the first few results I saw in Solr
    • For reference, the UID of the record I saw with duplicate metadata was: 50e52a06-ffb7-4597-8d92-1c608cc71c98

2021-01-13

  • I filed an issue on cg-core asking about how to handle series name / number
    • Currently the values are in format “series name; series number” in the dc.relation.ispartofseries field, but Peter wants to be able to separate them
  • Start working on CG Core v2 migration for DSpace 6, using my work from last year on DSpace 5

2021-01-14

  • More work on the CG Core v2 migration for DSpace 6
  • Publish v1.4.1 of the DSpace Statistics API based on feedback from the community
    • This includes the fix for limiting the Solr query to UUIDs

2021-01-17

  • 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" : 100540,
  "_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-2021-01-18
$ 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-2021-01-18'

2021-01-18

  • Finish the indexing on AReS that I started yesterday
  • Udana from IWMI emailed me to ask why the iwmi.csv doesn’t include items he approved to CGSpace this morning
    • I told him it is generated every Sunday night
    • I regenerated the file manually for him
    • I adjusted the script to run on Monday and Friday
  • Meeting with Peter and Abenet about CG Core v2
    • We also need to remove CTA and CPWF subjects from the input form since they are both closed now and no longer submitting items
    • Peter also wants to create new fields on CGSpace for the SDGs and CGIAR Impact Areas
      • I suggested cg.subject.sdg and cg.subject.impactArea
    • We also agreed to remove the following fields:
      • cg.livestock.agegroup
      • cg.livestock.function
      • cg.message.sms
      • cg.message.voice
    • I removed them from the input form, metadata registry, and deleted all the values in the database:
localhost/dspace63= > BEGIN;
localhost/dspace63= > DELETE FROM metadatavalue WHERE metadata_field_id IN (115, 116, 117, 118);
DELETE 27
localhost/dspace63= > COMMIT;
  • I submitted an issue to CG Core v2 to propose standardizing the camel case convention for a few more fields of ours
  • I submitted an issue to CG Core v2 to propose removing cg.series and cg.pages in favor of dcterms.isPartOf and dcterms.extent, respectively
  • It looks like we will roll all these changes into a CG Core v2.1 release

2021-01-19

  • Abenet said that the PDF reports on AReS aren’t working
    • I had to install unoconv in the backend api container again
$ docker exec -it api /bin/bash
# apt update && apt install unoconv
  • Help Peter get a list of titles and DOIs for CGSpace items that Altmetric does not have an attention score for
    • He generated a list from their dashboard and I extracted the DOIs in OpenRefine (because it was WINDOWS-1252 and csvcut couldn’t do it)
    • Then I looked up the titles and handles using the doi-to-handle.py script that I wrote last week
  • I created a pull request to convert several CG Core v2 fields to consistent “camel case”
  • I created a pull request to fix some links in cgcore.html

2021-01-21

  • File an issue for the OpenRXV backend API container’s missing unoconv
    • This causes PDF reports to not work, and I always have to go manually re-install it after rebooting the server
  • A little bit more work on the CG Core v2 migration in CGSpace
    • I updated the migrate-fields.sh script for DSpace 6 and created all the new fields in my test instance

2021-01-24

  • Abenet mentioned that Alan Duncan could not find one of his items on AReS, but it is on CGSpace
  • Import fifteen items to CGSpace for Peter after doing a brief check in OpenRefine and csv-metadata-quality
  • Ben Hack asked me why I’m still using the default favicon on CGSpace
  • 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" : 100699,
  "_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.b
locks.write":true}}'
$ curl -s -X POST http://localhost:9200/openrxv-items/_clone/openrxv-items-2021-01-25
$ 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-2021-01-25'
  • Resume working on CG Core v2, I realized a few things:
    • We are trying to move from dc.identifier.issn (and ISBN) to cg.issn, but this is currently implemented as a “qualdrop” input in DSpace’s submission form, which only works to fill in the qualifier (ie dc.identier.xxxx)
      • If we really want to use cg.issn and cg.isbn we would need to add a new input field for each separately
    • We are trying to move series name/number fro mdc.relation.ispartofseries to dcterms.isPartOf, but this uses a special “series” input type in DSpace’s submission form that joins series name and number with a colon (;)
      • If we really want to do that we need to add two separate input fields for each

2021-01-25

  • Finish indexing AReS and adjusting the indexes (see above)
  • Merged the changes for the favicon in to the 6_x-prod branch
  • Meeting with Peter and Abenet about CG Core v2
    • We agreed to go ahead with it ASAP and share a list of the changes with Macaroni, Fabio, and others and give them a firm timeline
    • We also discussed the CSV export option on DSpace 6 and were surprised to see that it kinda works
    • If you do a free-text search it works properly, but if you try to use the metadata filters it doesn’t
    • I changed the default setting to make it available to any logged in user and will deploy it on CGSpace this week

2021-01-26

  • Email some CIAT users who submitted items with upper case AGROVOC terms
    • I will do another global replace soon after they reply
  • Add CGIAR Impact Areas and UN Sustainable Development Goals (SDGs) to the 6x_prod branch
  • Looking into the issue with exporting search results in XMLUI again
    • I notice that there is an HTTP 400 when you try to export search results containing a filter
    • The Tomcat logs show:
Jan 26, 2021 10:47:23 AM org.apache.coyote.http11.AbstractHttp11Processor process
INFO: Error parsing HTTP request header
 Note: further occurrences of HTTP request parsing errors will be logged at DEBUG level.
java.lang.IllegalArgumentException: Invalid character found in the request target [/discover/search/csv?query=*&scope=~&filters=author:(Alan\%20Orth)]. The valid characters are defined in RFC 7230 and RFC 3986
        at org.apache.coyote.http11.InternalInputBuffer.parseRequestLine(InternalInputBuffer.java:213)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1108)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:654)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:317)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Thread.java:748)

# grep -E '26/Jan/2021:(08|09|10|11|12)' /var/log/nginx/rest.log | goaccess --log-format=COMBINED -
  • The culprit seems to be the ILRI publications importer, so that’s OK
  • But I also see an IP in Jordan hitting the REST API 1,100 times today:
80.10.12.54 - - [26/Jan/2021:09:43:42 +0100] "GET /rest/rest/bitstreams/98309f17-a831-48ed-8f0a-2d3244cc5a1c/retrieve HTTP/2.0" 302 138 "http://wp.local/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/87.0.4280.88 Safari/537.36"
  • Seems to be someone from CodeObia working on WordPress
    • I told them to please use a bot user agent so it doesn’t affect our stats, and to use DSpace Test if possible
  • I purged all ~3,000 statistics hits that have the “http://wp.local/" referrer:
$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>referrer:http\:\/\/wp\.local\/</query></delete>"

2021-01-27

  • Abenet approved my submission to CGSpace for the CSV metadata quality checker: https://hdl.handle.net/10568/110997
  • Add SDGs and Impact Areas to the XMLUI item display
  • Last week Atmire got back to me about the duplicates in Solr
    • The deduplicator appears to be working, but you need to limit the number of records, for example -r 100 so it doesn’t crash due to memory
    • They pointed to a few records solr_update_time_stamp:1605635765897 that have hundreds of duplicates which are now gone (still present if you look on the production server)
    • I need to try this again before doing it on CGSpace

2021-01-28

  • I did some more work on CG Core v2
    • I tested using cg.number twice in the submission form: once for journal issue, and once for series number
    • DSpace gets confused and ends up storing the number twice, even if you only enter it in one of the fields
    • I suggested to Marie that we use cg.issue for journal issue, since we’re already going to use cg.volume
    • That would free up cg.number for use by series number
  • I deployed the SDGs, Impact Areas, and favicon changes to CGSpace and posted a note on Yammer for the editors
    • Also ran all system updates and rebooted the server (linode18)

2021-01-31

  • AReS Explorer has been down since yesterday for some reason
    • First I ran all updates and rebooted the server (linode20)
    • Then start a re-index, first deleting the old Elasticsearch temp index:
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
# start indexing in AReS
  • Sent out emails about CG Core v2 to Macaroni Bros, Fabio, Hector at CCAFS, Dani and Tariku
  • A bit more minor work on testing the series/report/journal changes for CG Core v2