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Add notes for 2023-02-21
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@ -202,4 +202,130 @@ Done.
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- I think that particular error is because I applied the [indexes in this unmerged DSpace 6 patch](https://github.com/DSpace/DSpace/pull/1792), so I don't need to report this as an error in DSpace 7
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## 2023-02-16
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- I found a suspicious number of PostgreSQL locks on CGSpace and decided to investigate:
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```console
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$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
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44 dspaceApi
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372 dspaceCli
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446 dspaceWeb
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```
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- This started happening yesterday and I killed a few locks that were several hours old after inspecting the `locks-age.sql` output
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- I also checked the `locks.sql` output, which helpfully lists the blocked PID and the blocking PID, to find one blocking PID that was idle in transaction
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- I killed that process and then all other locks were instantly processed
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- I filed [a GitHub issue](https://github.com/DSpace/dspace-angular/issues/2103) on dspace-angular requesting the item view to use the bitstream description instead of the file name if present
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- Weekly CG Core types meeting
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- I need to go through the actions and remove those items that are only for CGSpace internal use, ie:
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- CD-ROM
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- Manuscript-unpublished
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- Photo Report
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- Questionnaire
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- Wiki
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- Weekly CGIAR Repository Working Group meeting
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- I did some experiments with Crossref dates for about 20,000 DOIs in CGSpace using my `crossref-doi-lookup.py` script
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- Some things I noted from reading the [Crossref API docs](https://github.com/CrossRef/rest-api-doc/blob/master/api_format.md) and inspecting the records for a few dozen DOIs manually:
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- `["created"]["date-parts"]` → Date on which the DOI was first registered (not useful for us)
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- `["published-print"]["date-parts"]` → Date on which the work was published in print
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- `["journal-issue"]["published-print"]["date-parts"]` → When present, is 99% the same as the above
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- `["published-online"]["date-parts"]` → Date on which the work was published online
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- `["journal-issue"]["published-online"]["date-parts"]` → Much more rare, and only 50% the same as the above, so unreliable
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- `["issued"]["date-parts"]` → Earliest of published-print and published-online (not useful to us)
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- After checking the DOIs manully I decided that when the `published-print` date exists, it is usually more accurate than our issued dates
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- I set 12,300 issue dates to those from Crossref
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- I also decided that, when `published-online` exists, it is usually accurate when I check the publisher page (we don't have many online dates to compare)
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- I set the available date for ~7,000 items to the published-online date as long as:
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- There was no `dcterms.available` date already
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- It was different than the issued date, because for now I only want online dates that are different, in case this is an online only journal in which case that can be the issue date... maybe I'll re-visit that later
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## 2023-02-17
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- It seems some (all?) of the changes I applied to dates last night didn't get saved...
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- I don't know what happened, so I will run them again after some investigation
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- I submitted the first batch of ~7,600 changes and it took twelve hours!
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- I almost cancelled it because after applying the changes there was a lock blocking everything for two hours, and it seemed to be stuck, but I kept checking it and saw that the `query_start` and `state_change` were being updated despite it being state "idle in transaction":
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```console
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$ psql -c 'SELECT * FROM pg_stat_activity WHERE pid=1025176' | less -S
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```
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- I will apply the other changes in smaller batches...
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- Lately I've noticed a lot of activity from the country code tagger curation task
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- Looking in the logs I see items being tagged that are very old and should have already been tagged years ago
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- Also, I see a ton of these errors whenever the task is updating an item:
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```console
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2023-02-17 08:01:00,252 INFO org.dspace.curate.Curator @ Curation task: countrycodetagger performed on: 10568/89020 with status: 0. Result: '10568/89020: added 1 alpha2 country code(s)'
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2023-02-17 08:01:00,467 ERROR com.atmire.versioning.ModificationLogger @ Error while writing item to versioning index: a0fe9d9a-6ac1-4b6a-8fcb-dae07a6bbf58 message:missing required field: epersonID
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org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: missing required field: epersonID
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at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
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at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
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at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
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at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
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at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:116)
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at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:102)
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at com.atmire.versioning.ModificationLogger.indexItem(ModificationLogger.java:263)
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at com.atmire.versioning.ModificationConsumer.end(ModificationConsumer.java:134)
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at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:157)
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at org.dspace.core.Context.dispatchEvents(Context.java:455)
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at org.dspace.curate.Curator.visit(Curator.java:541)
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at org.dspace.curate.Curator$TaskRunner.run(Curator.java:568)
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at org.dspace.curate.Curator.doCollection(Curator.java:515)
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at org.dspace.curate.Curator.doCommunity(Curator.java:487)
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at org.dspace.curate.Curator.doSite(Curator.java:451)
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at org.dspace.curate.Curator.curate(Curator.java:269)
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at org.dspace.curate.Curator.curate(Curator.java:203)
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at org.dspace.curate.CurationCli.main(CurationCli.java:220)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
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```
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- This must be related...
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## 2023-02-18
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- I realized why the country-code-tagger was tagging everything: I had overridden the `force` parameter last week!
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- Start a harvest on AReS
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## 2023-02-20
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- IWMI is concerned that some of their items with top Altmetric attention scores don't show up in the AReS Explorer
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- I looked into it for one and found that AReS is using the Handle, but Altmetric hasn't associated the Handle with the DOI
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- Looking into country and region issues for the PRMS team
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- Last week they had some questions about some invalid countries that ended up being typos
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- I realized my cgspace-java-helpers country-code-tagger curation task is not using the latest version, so it was missing Türkiye
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- I compiled the new version and ran it manually, but I have to upload a new version to Maven Central and then update the dependency in `dspace/modules/additions/pom.xml` ughhhhhh
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- I tagged version 6.2 with the change for Türkiye and uploaded to to Maven Central with `mvn clean deploy`
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- I'm having second thoughts about switching to UN M.49 for countries because there are just too many tradeoffs
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- I want to find a way to keep our existing list, and codify some rules for it
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- There are several discussions related to the shortcomings of ISO themselves and the iso-codes project, for example:
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- [Inconsistency with articles in ISO-3166-1 English short names](https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/33) (this one was filed by me two years ago!)
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- [ISO 3166-1: What's the policy for `common_name`?](https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/44)
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- I almost want to say fuck it, let's just use iso-codes and tell everyone to deal with it, but make sure we handle ISO 3166-1 Alpha2 or probably Alpha3 in the future
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- Something like:
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- Prefer `common_name` if it exists
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- Prefer the shorter of `name` and `official name`
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## 2023-02-21
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- Continue working on my `parse-iso-codes.py` script to parse the iso-codes JSON for ISO 3166-1
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- I also started a spreadsheet to track current CGSpace country names, proposed new names using the compromise above, and UN M.49 names
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- I proposed this to Peter but he wasn't happy because there are still some stupidly long and political names there
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- I bumped the version of cgspace-java-helpers to 6.2-SNAPSHOT and pushed it to Maven Central because I can't figure out how to get non-snapshot releases to go there
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- Ouch, grunt 1.6.0 was released a few weeks ago, which relies on Node.js v16, thus breaking the Mirage 2 build in DSpace 6
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- I filed [an issue in DSpace](https://github.com/DSpace/DSpace/issues/8676)
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- Help Moises from CIP troubleshoot harvesting issues on their WordPress site
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- I see 2,000 requests with the user agent "RTB website BOT" today and they are all HTTP 200
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```console
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# grep 'RTB website BOT' /var/log/nginx/rest.log | awk '{print $9}' | sort | uniq -c | sort -h
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2023 200
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```
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<!-- vim: set sw=2 ts=2: -->
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