cgspace-notes/content/posts/2020-04.md

---
title: "April, 2020"
date: 2020-04-02T10:53:24+03:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2020-04-02

- 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
  - I updated the fifty-eight existing items on CGSpace
- Looking into the items Udana had asked about last week that were missing Altmetric donuts:
  - [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

<!--more-->

- 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

## 2020-04-05

- 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%';"
DELETE 97
$ ./add-orcid-identifiers-csv.py -i 2020-04-07-peter-orcids.csv -db dspace -u dspace -p 'fuuu' -d
```

- 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"
"Ramirez-Villegas, Julian","Julian Ramirez-Villegas: 0000-0002-8044-583X"
"Villegas-Ramirez, J","Julian Ramirez-Villegas: 0000-0002-8044-583X"
"Ishitani, Manabu","Manabu Ishitani: 0000-0002-6950-4018"
"Manabu, Ishitani","Manabu Ishitani: 0000-0002-6950-4018"
"Ishitani, M.","Manabu Ishitani: 0000-0002-6950-4018"
"Ishitani, M.","Manabu Ishitani: 0000-0002-6950-4018"
"Buruchara, Robin A.","Robin Buruchara: 0000-0003-0934-1218"
"Buruchara, Robin","Robin Buruchara: 0000-0003-0934-1218"
"Jarvis, Andy","Andy Jarvis: 0000-0001-6543-0798"
"Jarvis, Andrew","Andy Jarvis: 0000-0001-6543-0798"
"Jarvis, A.","Andy Jarvis: 0000-0001-6543-0798"
"Tohme, Joseph M.","Joe Tohme: 0000-0003-2765-7101"
"Hansen, James","James Hansen: 0000-0002-8599-7895"
"Hansen, James W.","James Hansen: 0000-0002-8599-7895"
"Asseng, Senthold","Senthold Asseng: 0000-0002-7583-3811"
```

- 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:

```
$ ./add-orcid-identifiers-csv.py -i 2020-04-07-fix-duplicate-orcids.csv -db dspace -u dspace -p 'fuuu' -d
```

- I ran the fixes on DSpace Test and CGSpace as well
- 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

## 2020-04-12

- 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:

```
2020-04-12 16:34:33,363 ERROR com.atmire.dspace.app.xmlui.aspect.statistics.editorparts.DataTableTransformer @ java.lang.IllegalArgumentException: Invalid UUID string: 1
```

- And I remembered I actually need to run the DSpace 6.4 Solr UUID migrations:

```
$ export JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8"
$ ~/dspace63/bin/dspace solr-upgrade-statistics-6x
```

- 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!

## 2020-04-13

- 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:

```
$ export JAVA_OPTS="-Xmx2000m -Dfile.encoding=UTF-8"
$ ~/dspace63/bin/dspace solr-upgrade-statistics-6x -n 250000
```

- 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?):

```
$ podman rm artifactory
$ podman pull docker.bintray.io/jfrog/artifactory-oss:latest
$ podman create --ulimit nofile=32000:32000 --name artifactory -v artifactory_data:/var/opt/jfrog/artifactory -p 8081-8082:8081-8082 docker.bintray.io/jfrog/artifactory-oss
$ podman start artifactory
```

## 2020-04-14

- A few days ago Peter asked me to update an author's name on CGSpace and in the controlled vocabularies:

```
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...

## 2020-04-17

- 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

## 2020-04-20

- Looking into a high rate of outgoing bandwidth from yesterday on CGSpace (linode18):

```
# cat /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "19/Apr/2020:0[6789]" | goaccess --log-format=COMBINED -
```

- One host in Russia (91.241.19.70) download 23GiB over those few hours in the morning
  - It looks like all the requests were for one single item's bitstreams:

```
# grep -c 91.241.19.70 /var/log/nginx/access.log.1
8900
# grep 91.241.19.70 /var/log/nginx/access.log.1 | grep -c '10568/35187'
8900
```

- I thought the host might have been Yandex misbehaving, but its user agent is:

```
Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_3; nl-nl) AppleWebKit/527  (KHTML, like Gecko) Version/3.1.1 Safari/525.20
```

- I will purge that IP from the Solr statistics using my `check-spider-ip-hits.sh` script:

```
$ ./check-spider-ip-hits.sh -d -f /tmp/ip -p
(DEBUG) Using spider IPs file: /tmp/ip
(DEBUG) Checking for hits from spider IP: 91.241.19.70
Purging 8909 hits from 91.241.19.70 in statistics

Total number of bot hits purged: 8909
```

- While investigating that I noticed ORCID identifiers missing from a few authors names, so I added them with my `add-orcid-identifiers.py` script:

```
$ ./add-orcid-identifiers-csv.py -i 2020-04-20-add-orcids.csv -db dspace -u dspace -p 'fuuu' -d
```

- The contents of `2020-04-20-add-orcids.csv` was:

```
dc.contributor.author,cg.creator.id
"Schut, Marc","Marc Schut: 0000-0002-3361-4581"
"Schut, M.","Marc Schut: 0000-0002-3361-4581"
"Kamau, G.","Geoffrey Kamau: 0000-0002-6995-4801"
"Kamau, G","Geoffrey Kamau: 0000-0002-6995-4801"
"Triomphe, Bernard","Bernard Triomphe: 0000-0001-6657-3002"
"Waters-Bayer, Ann","Ann Waters-Bayer: 0000-0003-1887-7903"
"Klerkx, Laurens","Laurens Klerkx: 0000-0002-1664-886X"
```

- I confirmed some of the authors' names from the report itself, then by looking at their profiles on ORCID.org
- Add new ILRI subject "COVID19" to the `5_x-prod` branch
- Add new CCAFS Phase II project tags to the `5_x-prod` branch
- I will deploy these to CGSpace in the next few days

## 2020-04-24

- Atmire responded to my ticket about the  issue with glypicons and said their test server does not show this same issue
  - They asked if I am using the `JAVA_OPTS=-Dfile.encoding=UTF-8` when building DSpace and running Tomcat
  - I set it explicitly for Maven and Ant just now (and cleared all XMLUI caches) but the issue is still there
  - I asked them if they are building on macOS or Linux, and which Node.js version (I'm using 10.20.1, which is the current LTS branch).

## 2020-04-25

- 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:

```
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m"
$ time chrt -i 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
```

- I ran the `dspace cleanup -v` process on CGSpace and got an error:

```
Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
  Detail: Key (bitstream_id)=(184980) is still referenced from table "bundle".
```

- The solution is, as always:

```
$ psql -d dspace -U dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (183996);'
UPDATE 1
```

- 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:

```
.breadcrumb > li + li:before {
  content: "/\00a0";
}
```

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