- Maria asked me to update Charles Staver's ORCID iD in the submission template and on CGSpace, as his name was lower case before, and now he has corrected it
- [The first](https://hdl.handle.net/10568/103225) is still missing its DOI, so I added it and [tweeted its handle](https://twitter.com/mralanorth/status/1245632619661766657) (after a few hours there was a donut with score 222)
- [The second item](https://hdl.handle.net/10568/106899) now has a donut with score 2 since I [tweeted its handle](https://twitter.com/mralanorth/status/1243158045540134913) last week
- [The third item](https://hdl.handle.net/10568/107258) now has a donut with score 1 since I [tweeted it](https://twitter.com/mralanorth/status/1243158786392625153) last week
- On the same note, the [one item](https://hdl.handle.net/10568/106573) Abenet pointed out last week now has a donut with score of 104 after I [tweeted it](https://twitter.com/mralanorth/status/1243163710241345536) last week
- Altmetric responded about [one item](https://hdl.handle.net/10568/101286) that had no donut since at least 2019-12 and said they fixed some problems with their bot's user agent
- I decided to [tweet the item](https://twitter.com/mralanorth/status/1245703049445851140), as I can't remember if I ever did it before
- Update PostgreSQL JDBC driver to version 42.2.12
## 2020-04-07
- Yesterday Atmire sent me their [pull request for DSpace 6 modules](https://github.com/ilri/DSpace/pull/445)
- Peter pointed out that some items have his ORCID identifier (`cg.creator.id`) twice
- I think this is because my early `add-orcid-identifiers.py` script was adding identifiers to existing records without properly checking if there was already one present (at first it only checked if there was one with the exact `place` value)
- As a test I dropped all his ORCID identifiers and added them back with the `add-orcid-identifiers.py` script:
```
$ psql -h localhost -U postgres dspace -c "DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240 AND text_value LIKE '%Ballantyne%';"
- I used this CSV with the script (all records with his name have the name standardized like this):
```
dc.contributor.author,cg.creator.id
"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
```
- Then I tried another way, to identify all duplicate ORCID identifiers for a given resource ID and group them so I can see if count is greater than 1:
```
dspace=# \COPY (SELECT DISTINCT(resource_id, text_value) as distinct_orcid, COUNT(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 240 GROUP BY distinct_orcid ORDER BY count DESC) TO /tmp/2020-04-07-duplicate-orcids.csv WITH CSV HEADER;
COPY 15209
```
- Of those, about nine authors had duplicate ORCID identifiers over about thirty records, so I created a CSV with all their name variations and ORCID identifiers:
```
dc.contributor.author,cg.creator.id
"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
- Then I deleted *all* their existing ORCID identifier records:
```
dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240 AND text_value SIMILAR TO '%(0000-0001-6543-0798|0000-0001-9346-2893|0000-0002-6950-4018|0000-0002-7583-3811|0000-0002-8044-583X|0000-0002-8599-7895|0000-0003-0934-1218|0000-0003-2765-7101)%';
DELETE 994
```
- And then I added them again using the `add-orcid-identifiers` records:
- I started testing the [pull request](https://github.com/ilri/DSpace/pull/445) sent by Atmire yesterday
- I notice that we now need `yarn` to build, and I need to bump the Node.js `engine` version in our Mirage 2 theme in order to get it to build on Node.js 10.x
- Font Awesome icons for GitHub etc weren't loading, and after a bit of troubleshooting I replaced version 4.5.0 with 5.13.0 and to my surprise they now include Mendeley and ORCID so we can get rid of the Academicons dependency
- Testing the Atmire DSpace 6.3 code with a clean CGSpace DSpace 5.8 database snapshot
- One Flyway migration failed so I had to manually remove it (and of course create the pgcrypto extension):
```
dspace63=# DELETE FROM schema_version WHERE version IN ('5.8.2015.12.03.3');
dspace63=# CREATE EXTENSION pgcrypto;
```
- Then DSpace 6.3 started up OK and I was able to see some statistics in the Content and Usage Analysis (CUA) module, but not on community, collection, or item pages
- I also noticed at least one of these errors in the DSpace log:
- Run system updates on DSpace Test (linode26) and reboot it
- More work on the DSpace 6.3 stuff, improving the GDPR consent logic to use [haven](https://github.com/chiiya/haven) instead of cookieconsent
- It works better by injecting the Google Analytics script after the user clicks agree, and it also has a preferences section that gets automatically injected on the privacy page!
- I realized that `solr-upgrade-statistics-6x` only processes 100,000 records by default so I think we actually need to finish running it for all legacy Solr records before asking Atmire why CUA statlets and detailed statistics aren't working
- For now I am just doing 250,000 records at a time on my local environment:
- Despite running the migration for all of my local 1.5 million Solr records, I still see a few hundred thousand like `-1` and `0-unmigrated`
- I will purge them all and try to import only a subset...
- After importing again I see there are indeed tens of thousands of these documents with IDs "-1" and "0"
- They are all `type: 5`, which is "SITE" according to `Constants.java`:
```
/** DSpace site type */
public static final int SITE = 5;
```
- Even after deleting those documents and re-running `solr-upgrade-statistics-6x` I still get the UUID errors when using CUA and the statlets
- I have sent some feedback and questions to Atmire (including about the  issue with glypicons in the header trail)
- In other news, my local Artifactory container stopped working for some reason so I re-created it and it seems some things have changed upstream (port 8082 for web UI?):
dspace=# UPDATE metadatavalue SET text_value='Knight-Jones, Theodore J.D.' WHERE resource_type_id=2 AND metadata_field_id=3 AND text_value='Knight-Jones, T.J.D.';
```
- I updated his existing records on CGSpace, changed the controlled lists, added his ORCID identifier to the controlled list, and tagged his thirty-nine items with the ORCID iD
- The new DSpace 6 stuff that Atmire sent modifies the Mirage 2's `pom.xml` to copy the each theme's resulting `node_modules` to each theme after building and installing with `ant update` because they moved some packages from bower to npm and now reference them in `page-structure.xsl`
- This is a good idea, because bower is no longer supported, and npm has gotten a lot better, but it causes an extra 200,000 files to get copied!
- Most scripts are concatenated into `theme.js` during build, so we don't need the `node_modules` after that, but there are three scripts in `page-structure.xsl` that are not included there
- The scripts are a very old version of modernizr which is not even available on npm, html5shiv, and respond.js
- For modernizr I can simply download a static copy and put it in `0_CGIAR/scripts` and concatenate it into `theme.js`
- For the others, I can revert to using them from bower's `vendor` directory, which is installed by the parent XMLUI Mirage 2 theme
- During this process I also realized that `mvn clean` doesn't actually clean everything, and `dspace/modules/xmlui-mirage2/target` is remaining from previous builds and contains a bunch of shit from previous builds (including all the themes which I was trying to build without!)
- This must be a DSpace bug, but I should theoretically check on vanilla DSpace and then file a bug...
- Atmire responded to some of the issues I raised earlier this week about the DSpace 6 pull request
- They said they don't think the glyphicon encoding issue is due to their changes, but I built a new clean version of the vanilla `6_x-dev` branch from before their pull request and it *does not* have the encoding issue in the Mirage 2 header trails
- Also, they said we need to use something called `AtomicStatisticsUpdateCLI` to do the Solr legacy integer ID to UUID conversion so I asked for more information about that workflow
- I researched a bit more about the  issue with glypicons and realized it's due to [a bug in libsass](https://github.com/twbs/bootstrap-sass/issues/919)
- I have Ruby sass version 3.4.25 installed in my local environment, but DSpace Mirage 2 is supposed to build with 3.3.14
- Downgrading the version fixes it, though I wonder: why did I not have this issue on the `6.x-dev` branch before Atmire's pull request, and also on `5_x-prod` where I've been building for a few months here...
- I deployed the latest `5_x-prod` branch on CGSpace (linode18), ran all updates, and rebooted the server
- This includes the "COVID19" ILRI subject, the new CCAFS Phase II project tags, and the changes to an ILRI author name
- After restarting the server I had to restart Tomcat three times before all Solr statistics cores loaded properly.
- After that I started a full Discovery reindexing to pick up some author changes I made last week:
- I spent some time working on the XMLUI themes in DSpace 6
- Atmire's pull request modifies `pom.xml` to *not* exclude `node_modules`, which means an extra ~260,000 files get copied to our installation folder because of all the themes
- I worked on the `Gruntfile.js` to copy Font Awesome and Bootstrap glyphicon fonts out of `node_modules` and into `fonts` at build time, but still `jquery-ui.min.css` was being referenced as a `url()` in CSS
- SASS can include imported CSS in your compiled CSS—instead of including an `@import url(..)` if you import it without the ".css", but our version of Ruby SASS doesn't support that
- I hacked `Gruntfile.js` to use `dart-sass` instead of Ruby `compass` (including installing compass's mixins via npm!) but then [dart-sass converts all the glyphicon ASCII escape codes to Unicode literals](https://github.com/sass/dart-sass/issues/345) and they show up garbled in Firefox
- I tried to use `node-sass` instead of dart-sass and it doesn't replace the ASCII escapes with literals, but then I get the the  issue with the glyphicon in the header trail again! Back to square one!
- So that was a waste of five hours...
- I might just leave this [tiny hack](https://github.com/twbs/bootstrap-sass/issues/919) in `0_CGIAR/styles/_style.scss` to override this and be done with it: