cgspace-notes/content/2016-02.md

+++
date = "2016-02-05T13:18:00+03:00"
author = "Alan Orth"
title = "February, 2016"
tags = ["notes"]
image = "../images/bg.jpg"

+++
## 2016-02-05

- Looking at some DAGRIS data for Abenet Yabowork
- Lots of issues with spaces, newlines, etc causing the import to fail
- I noticed we have a very *interesting* list of countries on CGSpace:

![CGSpace country list](../images/2016/02/cgspace-countries.png)

- Not only are there 49,000 countries, we have some blanks (25)...
- Also, lots of things like "COTE D`LVOIRE" and "COTE D IVOIRE"

## 2016-02-06

- Found a way to get items with null/empty metadata values from SQL
- First, find the `metadata_field_id` for the field you want from the `metadatafieldregistry` table:

```
dspacetest=# select * from metadatafieldregistry;
```

- In this case our country field is 78
- Now find all resources with type 2 (item) that have null/empty values for that field:

```
dspacetest=# select resource_id from metadatavalue where resource_type_id=2 and metadata_field_id=78 and (text_value='' OR text_value IS NULL);
```

- Then you can find the handle that owns it from its `resource_id`:

```
dspacetest=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id = '22678';
```

- It's 25 items so editing in the web UI is annoying, let's try SQL!

```
dspacetest=# delete from metadatavalue where metadata_field_id=78 and text_value='';
DELETE 25
```

- After that perhaps a regular `dspace index-discovery` (no -b) *should* suffice...
- Hmm, I indexed, cleared the Cocoon cache, and restarted Tomcat but the 25 "|||" countries are still there
- Maybe I need to do a full re-index...
- Yep! The full re-index seems to work.
- Process the empty countries on CGSpace

## 2016-02-07

- Working on cleaning up Abenet's DAGRIS data with OpenRefine
- I discovered two really nice functions in OpenRefine: `value.trim()` and `value.escape("javascript")` which shows whitespace characters like `\r\n`!
- For some reason when you import an Excel file into OpenRefine it exports dates like 1949 to 1949.0 in the CSV
- I re-import the resulting CSV and run a GREL on the date issued column: `value.replace("\.0", "")`
- I need to start running DSpace in Mac OS X instead of a Linux VM
- Install PostgreSQL from homebrew, then configure and import CGSpace database dump:

```
$ postgres -D /opt/brew/var/postgres
$ createuser --superuser postgres
$ createuser --pwprompt dspacetest
$ createdb -O dspacetest --encoding=UNICODE dspacetest
$ psql postgres
postgres=# alter user dspacetest createuser;
postgres=# \q
$ pg_restore -O -U dspacetest -d dspacetest ~/Downloads/cgspace_2016-02-07.backup 
$ psql postgres
postgres=# alter user dspacetest nocreateuser;
postgres=# \q
$ vacuumdb dspacetest
$ psql -U dspacetest -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest -h localhost
```

- After building and running a `fresh_install` I symlinked the webapps into Tomcat's webapps folder:

```
$ mv /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT.orig
$ ln -sfv ~/dspace/webapps/xmlui /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT
$ ln -sfv ~/dspace/webapps/rest /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/rest
$ ln -sfv ~/dspace/webapps/jspui /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/jspui
$ ln -sfv ~/dspace/webapps/oai /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/oai
$ ln -sfv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/solr
$ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
```

- Add CATALINA_OPTS in `/opt/brew/Cellar/tomcat/8.0.30/libexec/bin/setenv.sh`, as this script is sourced by the `catalina` startup script
- For example:

```
CATALINA_OPTS="-Djava.awt.headless=true -Xms2048m -Xmx2048m -XX:MaxPermSize=256m -XX:+UseConcMarkSweepGC -Dfile.encoding=UTF-8"
```

- After verifying that the site is working, start a full index:

```
$ ~/dspace/bin/dspace index-discovery -b
```