cgspace-notes/content/posts/2018-04.md

---
title: "April, 2018"
date: 2018-04-01T16:13:54+02:00
author: "Alan Orth"
tags: ["Notes"]
---

## 2018-04-01

- I tried to test something on DSpace Test but noticed that it's down since god knows when
- Catalina logs at least show some memory errors yesterday:

<!--more-->

```
Mar 31, 2018 10:26:42 PM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run
SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]] 
java.lang.OutOfMemoryError: Java heap space

Exception in thread "ContainerBackgroundProcessor[StandardEngine[Catalina]]" java.lang.OutOfMemoryError: Java heap space
```

- So this is getting super annoying
- I ran all system updates on DSpace Test and rebooted it
- For some reason Listings and Reports is not giving any results for any queries now...
- I posted a message on Yammer to ask if people are using the Duplicate Check step from the Metadata Quality Module
- Help Lili Szilagyi with a question about statistics on some CCAFS items

## 2018-04-04

- Peter noticed that there were still some old CRP names on CGSpace, because I hadn't forced the Discovery index to be updated after I fixed the others last week
- For completeness I re-ran the CRP corrections on CGSpace:

```
$ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db dspace -u dspace -p 'fuuu'
Fixed 1 occurences of: AGRICULTURE FOR NUTRITION AND HEALTH
```

- Then started a full Discovery index:

```
$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx1024m'
$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b

real    76m13.841s
user    8m22.960s
sys     2m2.498s
```

- Elizabeth from CIAT emailed to ask if I could help her by adding ORCID identifiers to all of Joseph Tohme's items
- I used my [add-orcid-identifiers-csv.py](https://gist.githubusercontent.com/alanorth/a49d85cd9c5dea89cddbe809813a7050/raw/f67b6e45a9a940732882ae4bb26897a9b245ef31/add-orcid-identifiers-csv.py) script:

```
$ ./add-orcid-identifiers-csv.py -i /tmp/jtohme-2018-04-04.csv -db dspace -u dspace -p 'fuuu'
```

- The CSV format of `jtohme-2018-04-04.csv` was:

```csv
dc.contributor.author,cg.creator.id
"Tohme, Joseph M.",Joe Tohme: 0000-0003-2765-7101
```

- There was a quoting error in my CRP CSV and the replacements for `Forests, Trees and Agroforestry` got messed up
- So I fixed them and had to re-index again!
- I started preparing the git branch for the the DSpace 5.5→5.8 upgrade:

```
$ git checkout -b 5_x-dspace-5.8 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.8
```

- I was prepared to skip some commits that I had cherry picked from the upstream `dspace-5_x` branch when we did the DSpace 5.5 upgrade (see notes on 2016-10-19 and 2017-12-17):
  - [DS-3246] Improve cleanup in recyclable components (upstream commit on dspace-5_x: 9f0f5940e7921765c6a22e85337331656b18a403)
  - [DS-3250] applying patch provided by Atmire (upstream commit on dspace-5_x: c6fda557f731dbc200d7d58b8b61563f86fe6d06)
  - bump up to latest minor pdfbox version (upstream commit on dspace-5_x: b5330b78153b2052ed3dc2fd65917ccdbfcc0439)
  - DS-3583 Usage of correct Collection Array (#1731) (upstream commit on dspace-5_x: c8f62e6f496fa86846bfa6bcf2d16811087d9761)
- ... but somehow git knew, and didn't include them in my interactive rebase!
- I need to send this branch to Atmire and also arrange payment (see [ticket #560](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560) in their tracker)