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#!/usr/bin/env python
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Preparation for BioSQL tests, setting passwords etc
"""
import os
from Bio import MissingExternalDependencyError
from BioSQL import BioSeqDatabase
##################################
# Start of user-editable section #
##################################
# You are expected to edit the following lines to match your system.
# The BioSQL unit tests will call this code, and will only run if it works.
# Constants for the database driver
DBHOST = 'localhost'
DBUSER = 'root'
DBPASSWD = ''
TESTDB = 'biosql_test'
# -- MySQL
#DBDRIVER = 'MySQLdb'
#DBTYPE = 'mysql'
# -- PostgreSQL
#DBDRIVER = 'psycopg'
#DBTYPE = 'pg'
# -- SQLite
DBDRIVER = 'sqlite3'
DBTYPE = 'sqlite'
TESTDB = os.path.join(os.getcwd(), "BioSQL", "temp_sqlite.db")
# In memory SQLite does not work with current test structure since the tests
# expect databases to be retained between individual tests.
#TESTDB = ':memory:'
################################
# End of user-editable section #
################################
# Works for mysql and postgresql, not oracle
try:
DBSCHEMA = "biosqldb-" + DBTYPE + ".sql"
except NameError:
#This happens if the lines above are commented out
message = "Enter your settings in Tests/setup_BioSQL.py " \
"(not important if you do not plan to use BioSQL)."
raise MissingExternalDependencyError(message)
# Uses the SQL file in the Tests/BioSQL directory -- try to keep this current
# with what is going on with BioSQL
SQL_FILE = os.path.join(os.getcwd(), "BioSQL", DBSCHEMA)
assert os.path.isfile(SQL_FILE), "Missing %s" % SQL_FILE
#Check the database driver is installed:
try:
__import__(DBDRIVER)
except ImportError:
message = "Install %s or correct Tests/setup_BioSQL.py "\
"(not important if you do not plan to use BioSQL)." % DBDRIVER
raise MissingExternalDependencyError(message)
#Could check the username, password and host work here,
#but this only seems to work for the first unit test
#that tries to import this file.
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