cgspace-notes/content/posts/2019-12.md

---
title: "December, 2019"
date: 2019-12-01T11:22:30+02:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2019-12-01

- Upgrade CGSpace (linode18) to Ubuntu 18.04:
  - Check any packages that have residual configs and purge them:
  - <code># dpkg -l | grep -E '^rc' | awk '{print $2}' | xargs dpkg -P</code>
  - Make sure all packages are up to date and the package manager is up to date, then reboot:

```
# apt update && apt full-upgrade
# apt-get autoremove && apt-get autoclean
# dpkg -C
# reboot
```

<!--more-->

  - Take some backups:

```
# dpkg -l > 2019-12-01-linode18-dpkg.txt
# tar czf 2019-12-01-linode18-etc.tar.gz /etc
```
  - Then check all third-party repositories in /etc/apt to see if everything using "xenial" has packages available for "bionic" and then update the sources:
  - <code># sed -i 's/xenial/bionic/' /etc/apt/sources.list.d/*.list</code>
  - Pause the Uptime Robot monitoring for CGSpace
  - Make sure the update manager is installed and do the upgrade:

```
# apt install update-manager-core
# do-release-upgrade
```

  - After the upgrade finishes, remove Java 11, force the installation of bionic nginx, and reboot the server:

```
# apt purge openjdk-11-jre-headless
# apt install 'nginx=1.16.1-1~bionic'
# reboot
```

  - After the server comes back up, remove Python virtualenvs that were created with Python 3.5 and re-run certbot to make sure it's working:

```
# rm -rf /opt/eff.org/certbot/venv/bin/letsencrypt
# rm -rf /opt/ilri/dspace-statistics-api/venv
# /opt/certbot-auto
```

  - Clear Ansible's fact cache and re-run the playbooks to update the system's firewalls, SSH config, etc
- Altmetric finally responded to my question about Dublin Core fields
  - They shared a [list of fields they use for tracking](https://help.altmetric.com/support/solutions/articles/6000141419-what-metadata-is-required-to-track-our-content-), but it only mentions HTML meta tags, and not fields considered when harvesting via OAI
  - Anyways, there might be some areas we can improve on the HTML meta tags, if I look at one [item with a DOI, ISSN, etc](https://hdl.handle.net/10568/101623) I see that we could at least add status (Open Access) and journal title
  - I merged a [pull request](https://github.com/ilri/DSpace/pull/438) into the `5_x-prod` branch to add status and journal title to the XHTML meta tags

## 2019-12-02

- Raise the issue of old, low-quality thumbnails with Peter and the CGSpace team
  - I suggested that we move manually uploaded thumbnails from the `ORIGINAL` bundle to the `THUMBNAIL` bundle
  - Also replace old thumbnails where an item is available on Slideshare or YouTube because those are easy to get new, high-quality thumbnails for
- Continue testing CG Core v2 implementation on DSpace Test
  - Compare the OAI QDC representation of a few items on CGSpace vs DSpace Test:

```
$ http 'https://cgspace.cgiar.org/oai/request?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai:cgspace.cgiar.org:10568/104030' > /tmp/cgspace-104030.xml
$ http 'https://dspacetest.cgiar.org/oai/request?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai:cgspace.cgiar.org:10568/104030' > /tmp/dspacetest-104030.xml
```

  - The DSpace Test ones actually now capture the DOI, where the CGSpace doesn't...
  - And the DSpace Test one doesn't include review status as `dc.description`, but I don't think that's an important field 

## 2019-12-04

- Peter noticed that there were about seventy items on CGSpace that were marked as private
  - Some have been withdrawn, but I extracted a list of the forty-eight that were not:

```
dspace=# \COPY (SELECT handle, owning_collection FROM item, handle WHERE item.discoverable='f' AND item.in_archive='t' AND handle.resource_id = item.item_id) to /tmp/2019-12-04-CGSpace-private-items.csv WITH CSV HEADER;
COPY 48
```

## 2019-12-05

- Give [presentation about CG Core v2](https://hdl.handle.net/10568/106045) to the MEL Developers' Retreat in Nairobi, Kenya (via Skype)
- Send some pull requests to the cg-core schema repository:
  - [HTML syntax fixes](https://github.com/AgriculturalSemantics/cg-core/pull/16)
  - [Add LICENSE file](https://github.com/AgriculturalSemantics/cg-core/pull/17)
  - [Build main.css using npm build](https://github.com/AgriculturalSemantics/cg-core/pull/18)

## 2019-12-08

- Enrico noticed that the AReS Explorer on CGSpace (linode18) was down
  - I only see HTTP 502 in the nginx logs on CGSpace... so I assume it's something wrong with the AReS server
  - I ran all system updates on the AReS server (linode20) and rebooted it
  - After rebooting the Explorer was accessible again

## 2019-12-09

- Update PostgreSQL JDBC driver to [version 42.2.9](https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.9) in [Ansible playbooks](https://github.com/ilri/rmg-ansible-public)
  - Deploy on DSpace Test (linode19) to test before deploying on CGSpace in a few days
- Altmetric responded to my question about [the WLE item](https://hdl.handle.net/10568/97087) that has a lower score than its DOI
  - They say that they will "reprocess" the item "before Christmas"

## 2019-12-11

- Post [message to Yammer about good practices for thumbnails on CGSpace](https://www.yammer.com/dspacedevelopers/#/Threads/show?threadId=454830191804416)
  - On the topic of thumbnails, I'm thinking we might want to force regenerate all PDF thumbnails on CGSpace since we upgraded it to Ubuntu 18.04 and got a new ghostscript...
- More discussion about report formats for AReS
- Peter noticed that the Atmire reports weren't showing any statistics before 2019
  - I checked and indeed Solr had an issue loading some core last time it was started
  - I restarted Tomcat three times before all cores came up successfully
- While I was restarting the Tomcat service I upgraded the PostgreSQL JDBC driver to version 42.2.9, which had been deployed on DSpace Test earlier this week

## 2019-12-16

- Visit CodeObia office to discuss next phase of OpenRXV/AReS development
  - We discussed using CSV instead of Excel for tabular reports
    - OpenRXV should only have "simple" reports with Dublin Core fields
    - AReS should have this as well as a customized "extended" report that has CRPs, Subjects, Sponsors, etc from CGSpace
  - We discussed using RTF instead of Word for graphical reports

## 2019-12-17

- Start filing GitHub issues for the reporting features on OpenRXV and AReS
  - I created an issue for the "simple" tabular reports on OpenRXV GitHub ([#29](https://github.com/ilri/OpenRXV/issues/29))
  - I created an issue for the "extended" tabular reports on AReS GitHub ([#8](https://github.com/ilri/AReS/issues/8))
  - I created an issue for "simple" text reports on the OpenRXV GitHub ([#30](https://github.com/ilri/OpenRXV/issues/30))
  - I created an issue for "extended" text reports on the AReS GitHub ([#9](https://github.com/ilri/AReS/issues/9))
- I looked into creating RTF documents from HTML in Node.js and there is a library called [html-to-rtf](https://www.npmjs.com/package/html-to-rtf) that works well, but doesn't support images
- Export a list of all investors (`dc.description.sponsorship`) for Peter to look through and correct:

```
dspace=# \COPY (SELECT DISTINCT text_value as "dc.contributor.sponsor", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 29 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2019-12-17-investors.csv WITH CSV HEADER;
COPY 643
```

## 2019-12-18

- Apply the investor corrections and deletions from Peter on CGSpace:

```
$ ./fix-metadata-values.py -i /tmp/2019-12-17-investors-fix-112.csv -db dspace -u dspace -p 'fuuu' -f dc.description.sponsorship -m 29 -t correct -d
$ ./delete-metadata-values.py -i /tmp/2019-12-17-investors-delete-68.csv -db dspace -u dspace -p 'fuuu' -m 29 -f dc.description.sponsorship -d
```

- Peter asked about the "Open Government Licence 3.0" that is used by [some items]()
  - I notice that it [exists in SPDX as `UGL-UK-3.0`](https://spdx.org/licenses/OGL-UK-3.0.html) so I created a GitHub issue to add this to our controlled vocabulary ([#439](https://github.com/ilri/DSpace/issues/439))
  - I only see two in our database that use this for now, so I will update them:

```
dspace=# SELECT text_value FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=53 AND text_value LIKE '%Open%';
         text_value          
-----------------------------
 Open Government License 3.0
 Open Government License 3.0
(2 rows)
dspace=# UPDATE metadatavalue SET text_value='OGL-UK-3.0' WHERE resource_type_id=2 AND metadata_field_id=53 AND text_value LIKE '%Open Government License 3.0%';
UPDATE 2
```

- I created a pull request to add the license and merged it to the `5_x-prod` branch ([#440](https://github.com/ilri/DSpace/pull/440))
- Add three new CCAFS Phase II project tags to CGSpace ([#441](https://github.com/ilri/DSpace/pull/441))
- Linode said DSpace Test (linode19) had an outbound traffic rate of 73Mb/sec for the last two hours
  - I see some Russian bot active in nginx's access logs:

```
# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -c MegaIndex.ru 
27320
```

- I see they *did* check `robots.txt` and their requests are only going to XMLUI item pages... so I guess I just leave them alone
- Peter wrote to ask why this [one WLE item](https://cgspace.cgiar.org/handle/10568/101286) does [not have an Altmetric attention score](https://api.altmetric.com/v1/handle/10568/101286), but [the DOI does](https://api.altmetric.com/v1/doi/10.1126/science.aaw0911)
  - I tweeted the item just in case, but Peter said that he already did it yesterday
  - The item was added six months ago...
  - The DOI has an Altmetric score of 259, but for the Handle it is HTTP 404!
  - I emailed Altmetric support

## 2019-12-22

- I ran the `dspace cleanup` process on CGSpace (linode18) and had 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)=(179441) is still referenced from table "bundle".
```

- The solution is to delete that bitstream manually:

```
$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (179441);'
UPDATE 1
```

- Adjust [CG Core v2 migrataion notes]({{< relref "cgspace-cgcorev2-migration.md" >}}) to use `cg.review-status` instead of `cg.peer-reviewed`
  - I had [raised the issue](https://github.com/AgriculturalSemantics/cg-core/issues/14) with Marie-Angelique earlier this month
  - It makes much more sense to use a wider scope here than a simple boolean
- I also noticed another field that we should be using in DCTERMS instead of CG: `cg.targetaudience`
  - [DCTERMS says that `dcterms.audience` should be used to describe a A class of entity for whom the resource is intended or useful."](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/2012-06-14/?v=terms#audience)
  - I will update my notes for this so that we use that field instead
  - I don't see "audience" on the [cg-core](https://github.com/AgriculturalSemantics/cg-core/) repository so I filed [an issue](https://github.com/AgriculturalSemantics/cg-core/issues/19) to raise it with Marie-Angelique

## 2019-12-23

- Follow up with Altmetric on the issue where [an item](https://hdl.handle.net/10568/97087) has a different (lower) score for its Handle despite it having a correct DOI (with a higher score)
  - I've raised this issue three times to Altmetric this year, and a few weeks ago they said they would re-process the item "before Christmas"
- Abenet suggested we use `cg.reviewStatus` instead of `cg.review-status` and I agree that we should follow other examples like `DCTERMS.accessRights` and `DCTERMS.isPartOf`
  - I updated [my comment on the cg-core issue on GitHub](https://github.com/AgriculturalSemantics/cg-core/issues/14)

## 2019-12-30

- Altmetric responded a few days ago about the [item](https://hdl.handle.net/10568/97087) that has a different (lower) score for its Handle despite it having a correct DOI (with a higher score)
  - She tweeted the repository link and agreed that it didn't get picked up by Altmetric
  - She said she will add this to the existing ticket about the previous items I had raised an issue about
- Update Tomcat to version 7.0.99 in the [Ansible infrastructure playbooks](https://github.com/ilri/rmg-ansible-public) and deploy on DSpace Test (linode19)

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