--- title: "February, 2023" date: 2023-02-01T10:57:36+03:00 author: "Alan Orth" categories: ["Notes"] --- ## 2023-02-01 - Export CGSpace to cross check the DOI metadata with Crossref - I want to try to expand my use of their data to journals, publishers, volumes, issues, etc... - First, extract a list of DOIs for use with `crossref-doi-lookup.py`: ```console $ csvcut -c 'cg.identifier.doi[en_US]' ~/Downloads/2023-02-01-cgspace.csv \ | csvgrep -c 1 -m 'doi.org' \ | csvgrep -c 1 -m ' ' -i \ | csvgrep -c 1 -r '.*cifor.*' -i \ | sed 1d > /tmp/2023-02-01-dois.txt $ ./ilri/crossref-doi-lookup.py -e a.orth@cgiar.org -i /tmp/2023-02-01-dois.txt -o ~/Downloads/2023-01-31-crossref-results.csv -d ``` - Then extract the ID, DOI, journal, volume, issue, publisher, etc from the CGSpace dump and rename the `cg.identifier.doi[en_US]` to `doi` so we can join on it with the Crossref results file: ```console $ csvcut -c 'id,cg.identifier.doi[en_US],cg.journal[en_US],cg.volume[en_US],cg.issue[en_US],dcterms.publisher[en_US],cg.number[en_US],dcterms.license[en_US]' ~/Downloads/2023-02-01-cgspace.csv \ | csvgrep -c 'cg.identifier.doi[en_US]' -r '.*cifor.*' -i \ | sed -e '1s/cg.identifier.doi\[en_US\]/doi/' \ -e 's_https://doi.org/__g' \ -e 's_https://dx.doi.org/__g' \ > /tmp/2023-02-01-cgspace-doi-metadata.csv $ csvjoin -c doi /tmp/2023-02-01-cgspace-doi-metadata.csv ~/Downloads/2023-02-01-crossref-results.csv > /tmp/2023-02-01-cgspace-crossref-check.csv ``` - And import into OpenRefine for analysis and cleaning - I just noticed that Crossref also has types, so we could use that in the future too! - I got a few corrections after examining manually, but I didn't manage to identify any patterns that I could use to do any automatic matching or cleaning ## 2023-02-05 - Normalize text lang attributes in PostgreSQL, run a quick Discovery index, and then export CGSpace to check Initiative mappings and countries/regions - Run all system updates on CGSpace (linode18) and reboot it ## 2023-02-06 - Peter said that a new Initiative was approved last month so we need to add it to CGSpace: `Fragility, Conflict, and Migration` - There is lots of discussion about the "issue date" versus "available date" with Enrico and IFPRI, after lots of feedback from the PRMS QA - I filed [an issue on CG Core to propose using `dcterms.available` as an optional field to indicate the online date](https://github.com/AgriculturalSemantics/cg-core/issues/43) ## 2023-02-07 - IFPRI's web developer Tony managed to get his Drupal harvester to have a useful user agent: ```console 54.x.x.x - - [06/Feb/2023:10:10:32 +0100] "POST /rest/items/find-by-metadata-field?limit=%22100&offset=0 HTTP/1.1" 200 58855 "-" "IFPRI drupal POST harvester" ``` - He also noticed that there is no pagination on POST requests to `/rest/items/find-by-metadata-field`, and that he needs to increase his timeout for requests that return 100+ results, ie: ```console curl -f -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.actionArea", "value":"Systems Transformation", "language": "en_US"}' ``` - I need to ask on the DSpace Slack about this POST pagination - Abenet and Udana noticed that the Handle server was not running - Looking in the `error.log` file I see that the service is complaining about a lock file being present - This is because Linode had to do emergency maintenance on the VM host this morning and the Handle server didn't shut down properly - I'm having an issue with `poetry update` so I spent some time debugging and filed [an issue](https://github.com/python-poetry/poetry/issues/7482) - Proof and import nine items for the Digital Innovation Inititive for IFPRI - There were only some minor issues in the metadata - I also did a duplicate check with `check-duplicates.py` just in case - I did some minor updates on csv-metadata-quality - First, to reduce warnings on non-SPDX licenses like "Copyrighted; all rights reserved" and "Other" since they are very common for us and I'm sick of seeing the warnings - Second, to skip whitespace and newline fixes on the abstract field since so many times they are intended ## 2023-02-08 - Make some edits to IFPRI records requested by Jawoo and Leigh - Help Alessandra upload a last minute report for SAPLING - Proof and upload twenty-seven IFPRI records to CGSpace - It's a good thing I did a duplicate check because I found three duplicates! - Export CGSpace to update Initiative mappings and country/region mappings - Then start a harvest on AReS ## 2023-02-09 - Do some minor work on the CSS on the DSpace 7 test ## 2023-02-10 - I noticed a large number of PostgreSQL locks from dspaceWeb on CGSpace: ```console $ 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 2033 dspaceWeb ``` - Looking at the lock age, I see some already 1 day old, including this curious query: ```console select nextval ('public.registrationdata_seq') ``` - I killed all locks that were more than a few hours old - Export CGSpace to update Initiative collection mappings - Discuss adding `dcterms.available` to the submission form - I also looked in the `dcterms.description` field on CGSpace and found ~1,500 items where the is an indication of an online published date - Using some facets in OpenRefine I narrowed down the ones mentioning "online" and then extracted the dates to a new column: ```console cells['dcterms.description[en_US]'].value.replace(/.*?(\d+{2}) ([a-zA-Z]+) (\d+{2}).*/,"$3-$2-$1") ``` - Then to handle formats like "2022-April-26" and "2021-Nov-11" I used some replacement GRELs (note the order so we don't replace short patterns in longer strings prematurely): ```console value.replace("January","01").replace("February","02").replace("March","03").replace("April","04").replace("May","05").replace("June","06").replace("July","07").replace("August","08").replace("September","09").replace("October","10").replace("November","11").replace("December","12") value.replace("Jan","01").replace("Feb","02").replace("Mar","03").replace("Apr","04").replace("May","05").replace("Jun","06").replace("Jul","07").replace("Aug","08").replace("Sep","09").replace("Oct","10").replace("Nov","11").replace("Dec","12") ``` - This covered about 1,300 items, then I did about 100 more messier ones with some more regex wranling - I removed the `dcterms.description[en_US]` field from items where I updated the dates - Then I added `dcterms.available` to the submission form and the item view - We need to announce this to the editors ## 2023-02-13 - Export CGSpace to do some metadata quality checks - I added CGIAR Trust Fund as a donor to some new Initiative outputs - I moved some abstracts from the description field - I moved some version information to the `cg.edition` field ## 2023-02-14 - The PRMS team in Colombia sent some questions about countries on CGSpace - I had to fix some, that were clearly wrong, but there is also a difference between CGSpace and MEL because we use mostly iso-codes, and MEL uses the UN M.49 list - Then I re-ran the country code tagger from cgspace-java-helpers, forcing the update on all items in the Initiatives community - Remove Alliance research levers from `cg.contributor.crp` field after discussing with Daniel and Maria - This was a mistake on TIP's part, and there is no direct mapping between research levers and CRPs - I exported CGSpace to check Initiative collection mappings, regions, and licenses - Peter told me that all CGIAR blog posts for the Initiatives should be CC-BY-4.0, and I see the logo at the bottom in light gray! - I had previously missed that and removed some licenses for blog posts - I checked cgiar.org, ifpri.org, icarda.org, iwmi.cgiar.org, irri.org, etc and corrected a handful - Start a harvest on AReS ## 2023-02-15 - Work on rebasing my local DSpace 7 dev branches on top of the latest 7.5-SNAPSHOT - It seems the issues I had with the `dspace submission-forms-migrate` tool in [August, 2022]({{< relref "2022-08.md" >}}) were fixed - I imported a fresh PostgreSQL snapshot from CGSpace and then removed the Atmire migrations and ran the new migrations as I originally noted in [March, 2022]({{< relref "2022-03.md" >}}), and is pointed out in the [DSpace 7 upgrade notes](https://wiki.lyrasis.org/display/DSDOC7x/Upgrading+DSpace) - Now I get a new error: ```console localhost/dspace7= ☘ DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25'); localhost/dspace7= ☘ DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%'; localhost/dspace7= \q $ ./bin/dspace database migrate ignored ... CREATE INDEX resourcepolicy_action_idx ON resourcepolicy(action_id) at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.handleException(DefaultSqlScriptExecutor.java:275) at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.executeStatement(DefaultSqlScriptExecutor.java:222) at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.execute(DefaultSqlScriptExecutor.java:126) at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.executeOnce(SqlMigrationExecutor.java:69) at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.lambda$execute$0(SqlMigrationExecutor.java:58) at org.flywaydb.core.internal.database.DefaultExecutionStrategy.execute(DefaultExecutionStrategy.java:27) at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.execute(SqlMigrationExecutor.java:57) at org.flywaydb.core.internal.command.DbMigrate.doMigrateGroup(DbMigrate.java:377) ... 24 more Caused by: org.postgresql.util.PSQLException: ERROR: relation "resourcepolicy_action_idx" already exists at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2676) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2366) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:356) at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413) at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:333) at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:319) at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:295) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:290) at org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:193) at org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:193) at org.flywaydb.core.internal.jdbc.JdbcTemplate.executeStatement(JdbcTemplate.java:201) at org.flywaydb.core.internal.sqlscript.ParsedSqlStatement.execute(ParsedSqlStatement.java:95) at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.executeStatement(DefaultSqlScriptExecutor.java:210) ... 30 more ``` - I dropped that index and then the migration succeeded: ```console localhost/dspace7= ☘ DROP INDEX resourcepolicy_action_idx; localhost/dspace7= ☘ \q $ ./bin/dspace database migrate ignored Done. ``` - 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 ## 2023-02-16 - I found a suspicious number of PostgreSQL locks on CGSpace and decided to investigate: ```console $ 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 44 dspaceApi 372 dspaceCli 446 dspaceWeb ``` - This started happening yesterday and I killed a few locks that were several hours old after inspecting the `locks-age.sql` output - 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 - I killed that process and then all other locks were instantly processed - 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 - Weekly CG Core types meeting - I need to go through the actions and remove those items that are only for CGSpace internal use, ie: - CD-ROM - Manuscript-unpublished - Photo Report - Questionnaire - Wiki - Weekly CGIAR Repository Working Group meeting - I did some experiments with Crossref dates for about 20,000 DOIs in CGSpace using my `crossref-doi-lookup.py` script - 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: - `["created"]["date-parts"]` → Date on which the DOI was first registered (not useful for us) - `["published-print"]["date-parts"]` → Date on which the work was published in print - `["journal-issue"]["published-print"]["date-parts"]` → When present, is 99% the same as the above - `["published-online"]["date-parts"]` → Date on which the work was published online - `["journal-issue"]["published-online"]["date-parts"]` → Much more rare, and only 50% the same as the above, so unreliable - `["issued"]["date-parts"]` → Earliest of published-print and published-online (not useful to us) - After checking the DOIs manully I decided that when the `published-print` date exists, it is usually more accurate than our issued dates - I set 12,300 issue dates to those from Crossref - 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) - I set the available date for ~7,000 items to the published-online date as long as: - There was no `dcterms.available` date already - 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 ## 2023-02-17 - It seems some (all?) of the changes I applied to dates last night didn't get saved... - I don't know what happened, so I will run them again after some investigation - I submitted the first batch of ~7,600 changes and it took twelve hours! - 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": ```console $ psql -c 'SELECT * FROM pg_stat_activity WHERE pid=1025176' | less -S ``` - I will apply the other changes in smaller batches... - Lately I've noticed a lot of activity from the country code tagger curation task - Looking in the logs I see items being tagged that are very old and should have already been tagged years ago - Also, I see a ton of these errors whenever the task is updating an item: ```console 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)' 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 org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: missing required field: epersonID at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552) at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210) at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206) at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124) at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:116) at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:102) at com.atmire.versioning.ModificationLogger.indexItem(ModificationLogger.java:263) at com.atmire.versioning.ModificationConsumer.end(ModificationConsumer.java:134) at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:157) at org.dspace.core.Context.dispatchEvents(Context.java:455) at org.dspace.curate.Curator.visit(Curator.java:541) at org.dspace.curate.Curator$TaskRunner.run(Curator.java:568) at org.dspace.curate.Curator.doCollection(Curator.java:515) at org.dspace.curate.Curator.doCommunity(Curator.java:487) at org.dspace.curate.Curator.doSite(Curator.java:451) at org.dspace.curate.Curator.curate(Curator.java:269) at org.dspace.curate.Curator.curate(Curator.java:203) at org.dspace.curate.CurationCli.main(CurationCli.java:220) 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) ``` - This must be related... ## 2023-02-18 - I realized why the country-code-tagger was tagging everything: I had overridden the `force` parameter last week! - Start a harvest on AReS ## 2023-02-20 - IWMI is concerned that some of their items with top Altmetric attention scores don't show up in the AReS Explorer - I looked into it for one and found that AReS is using the Handle, but Altmetric hasn't associated the Handle with the DOI - Looking into country and region issues for the PRMS team - Last week they had some questions about some invalid countries that ended up being typos - I realized my cgspace-java-helpers country-code-tagger curation task is not using the latest version, so it was missing Türkiye - 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 - I tagged version 6.2 with the change for Türkiye and uploaded to to Maven Central with `mvn clean deploy` - I'm having second thoughts about switching to UN M.49 for countries because there are just too many tradeoffs - I want to find a way to keep our existing list, and codify some rules for it - There are several discussions related to the shortcomings of ISO themselves and the iso-codes project, for example: - [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!) - [ISO 3166-1: What's the policy for `common_name`?](https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/44) - 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 - Something like: - Prefer `common_name` if it exists - Prefer the shorter of `name` and `official name` ## 2023-02-21 - Continue working on my `parse-iso-codes.py` script to parse the iso-codes JSON for ISO 3166-1 - I also started a spreadsheet to track current CGSpace country names, proposed new names using the compromise above, and UN M.49 names - I proposed this to Peter but he wasn't happy because there are still some stupidly long and political names there - 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 - 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 - I filed [an issue in DSpace](https://github.com/DSpace/DSpace/issues/8676) - Help Moises from CIP troubleshoot harvesting issues on their WordPress site - I see 2,000 requests with the user agent "RTB website BOT" today and they are all HTTP 200 ```console # grep 'RTB website BOT' /var/log/nginx/rest.log | awk '{print $9}' | sort | uniq -c | sort -h 2023 200 ```