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
```

## 2016-02-08

- Finish cleaning up and importing ~400 DAGRIS items into CGSpace
- Whip up some quick CSS to make the button in the submission workflow use the XMLUI theme's brand colors ([#154](https://github.com/ilri/DSpace/issues/154))

![ILRI submission buttons](../images/2016/02/submit-button-ilri.png)
![Drylands submission buttons](../images/2016/02/submit-button-drylands.png)

## 2016-02-09

- Re-sync DSpace Test with CGSpace
- Help Sisay with OpenRefine
- Enable HTTPS on DSpace Test using Let's Encrypt:

```
$ cd ~/src/git
$ git clone https://github.com/letsencrypt/letsencrypt
$ cd letsencrypt
$ sudo service nginx stop
# add port 443 to firewall rules
$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
$ sudo service nginx start
$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass
```

- We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: https://letsencrypt.org/howitworks/
- I had to export some CIAT items that were being cleaned up on the test server and I noticed their `dc.contributor.author` fields have DSpace 5 authority index UUIDs...
- To clean those up in OpenRefine I used this GREL expression: `value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")`
- Getting more and more hangs on DSpace Test, seemingly random but also during CSV import
- Logs don't always show anything right when it fails, but eventually one of these appears:

```
org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space
```

- or

```
Caused by: java.util.NoSuchElementException: Timeout waiting for idle object
```

- Right now DSpace Test's Tomcat heap is set to 1536m and we have quite a bit of free RAM:

```
# free -m
             total       used       free     shared    buffers     cached
Mem:          3950       3902         48          9         37       1311
-/+ buffers/cache:       2552       1397
Swap:          255         57        198
```

- So I'll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)

## 2016-02-11

- Massaging some CIAT data in OpenRefine
- There are 1200 records that have PDFs, and will need to be imported into CGSpace
- I created a `filename` column based on the `dc.identifier.url` column using the following transform:

```
value.split('/')[-1]
```

- Then I wrote a tool called [`generate-thumbnails.py`](https://gist.github.com/alanorth/2206f24483fe5f0454fc) to download the PDFs and generate thumbnails for them, for example:

```
$ ./generate-thumbnails.py ciat-reports.csv
Processing 64661.pdf
> Downloading 64661.pdf
> Creating thumbnail for 64661.pdf
Processing 64195.pdf
> Downloading 64195.pdf
> Creating thumbnail for 64195.pdf
```

## 2016-02-12

- Looking at CIAT's records again, there are some problems with a dozen or so files (out of 1200)
- A few items are using the same exact PDF
- A few items are using HTM or DOC files
- A few items link to PDFs on IFPRI's e-Library or Research Gate
- A few items have no item
- Also, I'm not sure if we import these items, will be remove the `dc.identifier.url` field from the records?

## 2016-02-12

- Looking at CIAT's records again, there are some files linking to PDFs on Slide Share, Embrapa, UEA UK, and Condesan, so I'm not sure if we can use those
- 265 items have dirty, URL-encoded filenames:

```
$ ls | grep -c -E "%"
265
```

- I suggest that we import ~850 or so of the clean ones first, then do the rest after I can find a clean/reliable way to decode the filenames
- This python2 snippet seems to work in the CLI, but not so well in OpenRefine:

```
$ python -c "import urllib, sys; print urllib.unquote(sys.argv[1])" CIAT_COLOMBIA_000169_T%C3%A9cnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_yuca.pdf
CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_yuca.pdf
```

- Merge pull requests for submission form theming ([#178](https://github.com/ilri/DSpace/pull/178)) and missing center subjects in XMLUI item views ([#176](https://github.com/ilri/DSpace/pull/176))
- They will be deployed on CGSpace the next time I re-deploy