[BioSQL-l] load_ncbi_taxonomy.pl for DB2

[Florian Mittag]

Hi everyone!

I just completed and tested the changes we've made on the 
load_ncbi_taxonomy.pl script from BioSQL 1.0.1.

Basically, only 3 changes were necessary, but some things have to be 
considered when running the script:

1) Although DB2 v9.7 supports TRUNCATE TABLE, when I specify 
the --allow_truncate option the script gave me the error SQL0428N "The SQL 
statement is only allowed as the first statement in a unit of work."
(https://publib.boulder.ibm.com/infocenter/db2luw/v9r7/index.jsp?topic=/com.ibm.db2.luw.messages.sql.doc/doc/msql00428n.html)

My solution is to just not set allow_truncate, so the script will use a DELETE 
command.

2) Specifying hostname and port will lead to an error saying that the database 
wasn't found. Searching the web I found information suggesting that you have 
to add a remote database to the catalog (or something) on the server and the 
client and then you are able to point to the database through its name.

My solution is to run the script on the machine where the DB2 instance is 
running and everything is fine.


I've run into some other problems before, but those were mostly caused by me 
forgetting to set the right environment variables, so that shouldn't be a 
problem for someone who actually knows something about DB2 ;-)


I hope this helps. As for the database schema for DB2, we have scripts to 
create the database with all its tables and constraints, but as you might see 
from my other posts here, we're not completely done and have to do more 
tests.


Now, I'm awaiting your feedback ;-)

Regards,
  Florian
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