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:

• 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)

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 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) and missing center subjects in XMLUI item views (#176)
• They will be deployed on CGSpace the next time I re-deploy