Testing Taxadb

You can easily run some tests. To do so proceed as follow:

cd /path/to/taxadb
nosetests

This simple command will run tests against an SQLite test database called test_db.sqlite located in taxadb/test directory.

It is also possible to only run tests related to accessionid or taxid as follow

nosetests -a 'taxid'
nosetests -a 'accessionid'

You can also use the configuration file located in root distribution taxadb.ini as follow. This file should contains database connection settings:

nosetests --tc-file taxadb.ini

You can override configuration file settings using command line options –tc such as:

nosetest --tc-file taxadb.ini --tc=sql.dbname:another_dbname

More info at nose-testconfig.

Running tests against PostgreSQL or MySQL

First create a test database to insert test data

  • PostgreSQL
createdb <test_db>

or from PostgreSQL client psql

psql -U postgres
psql> CREATE DATABASE <test_db>;
  • MySQL
mysql -u root
mysql> CREATE DATABASE <test_db>;

Load test data

  • PostgreSQL
gunzip -c /path/to/taxadb/taxadb/test/test_mypg_db.sql.gz | psql -d <test_db> -U <user>
  • MySQL
gunzip -c /path/to/taxadb/taxadb/test/test_mypg_db.sql.gz | mysql -D <test_db> -u <user> -p

Run tests

Either edit taxadb.ini to fit database configuration or use –tc command line option and set appropriate values like username, password, port, hostname, dbtype(postgres or mysql), dbname.

  1. PostgreSQL
nosetests --tc-file taxadb.ini

nosetests -tc-file taxadb.ini --tc=sql.dbtype:postgres --tc=sql.username:postgres --tc=sql.dbname:test_db2
  1. MySQL
nosetests --tc-file taxadb.ini

nosetests -tc-file taxadb.ini --tc=sql.dbtype:mysql --tc=sql.username:root --tc=sql.dbname:newdbname