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
```

- 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
```
Add notes for 2018-04-01 2018-04-01 16:21:41 +02:00			`---`
			`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`
Add notes for 2018-04-04 2018-04-04 14:57:34 +02:00
			`## 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`
			```

			`- 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`
			```