#!/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 = 'psycopg2' #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.