def setup(self):
# test will be skipped if unavailable
import MySQLdb
createTable = """\
CREATE TABLE test.sqlsequence_test (primary_id INTEGER PRIMARY KEY AUTO_INCREMENT, sequence TEXT)
"""
try:
self.db = sqlgraph.SQLTable('test.sqlsequence_test',
dropIfExists=True,
createTable=createTable,
attrAlias=dict(seq='sequence'))
except MySQLdb.MySQLError:
tempcurs = sqlgraph.getNameCursor()[1]
try: # hmm, maybe need to create the test database?
tempcurs.execute('create database if not exists test')
self.db = sqlgraph.SQLTable('test.sqlsequence_test',
dropIfExists=True,
createTable=createTable,
attrAlias=dict(seq='sequence'))
except MySQLdb.MySQLError: # no server, database or privileges?
print """\
The MySQL 'test' database doesn't exist and/or can't be
created or accessed on this account. This test will be skipped.
"""
raise ImportError # skip tests.
self.db.cursor.execute("""\
INSERT INTO test.sqlsequence_test (sequence)
VALUES ('CACCCTGCCCCATCTCCCCAGCCTGGCCCCTCGTGTCTCAGAACCCTCGGGGGGAGGCACAGAAGCCTTCGGGG')
""")
self.db.cursor.execute("""\
INSERT INTO test.sqlsequence_test (sequence)
VALUES ('GAAAGAAAGAAAGAAAGAAAGAAAGAGAGAGAGAGAGACAGAAG')
""")
class DNASeqRow(seqdb.DNASQLSequence):
def __len__(self): # just speed optimization
return self._select('length(sequence)') # SQL SELECT expression
self.db.objclass(DNASeqRow) # force the table object to return DNASeqRow objects
self.row1 = self.db[1]
self.row2 = self.db[2]
def setup(self):
from pygr import sqlgraph
import MySQLdb # test will be skipped if unavailable
createOpts = dict(source_id='int', target_id='int', edge_id='int')
try:
self.datagraph = sqlgraph.SQLGraph('test.dumbo_foo_test',
dropIfExists=True,
createTable=createOpts)
except MySQLdb.MySQLError:
tempcurs = sqlgraph.getNameCursor()[1]
try: # hmm, maybe need to create the test database
tempcurs.execute('create database if not exists test')
self.datagraph = sqlgraph.SQLGraph('test.dumbo_foo_test',
dropIfExists=True,
createTable=createOpts)
except MySQLdb.MySQLError: # no server, database or privileges?
print """The MySQL 'test' database doesn't exist and/or can't be
created or accessed on this account. This test will be skipped
"""
raise ImportError # skip tests.
def setup(self):
# test will be skipped if unavailable
import MySQLdb
createTable = """\
CREATE TABLE test.sqltable_test (primary_id INTEGER PRIMARY KEY AUTO_INCREMENT, seq_id TEXT, start INTEGER, stop INTEGER)
"""
try:
self.db = SQLTable('test.sqltable_test',
dropIfExists=True,
createTable=createTable)
except MySQLdb.MySQLError:
tempcurs = getNameCursor()[1]
try: # hmm, maybe need to create the test database?
tempcurs.execute('create database if not exists test')
self.db = SQLTable('test.sqltable_test',
dropIfExists=True,
createTable=createTable)
except MySQLdb.MySQLError: # no server, database or privileges?
print """\
The MySQL 'test' database doesn't exist and/or can't be
created or accessed on this account. This test will be skipped.
"""
raise ImportError # skip tests.
self.db.cursor.execute("""\
INSERT INTO test.sqltable_test (seq_id, start, stop)
VALUES ('seq1', 0, 10)
""")
self.db.cursor.execute("""\
INSERT INTO test.sqltable_test (seq_id, start, stop)
VALUES ('seq2', 5, 15)
""")
self.sourceDB = SQLTable('test.sqltable_join1',
dropIfExists=True, createTable="""\
CREATE TABLE test.sqltable_join1 (my_id INTEGER PRIMARY KEY,
other_id VARCHAR(16))
""")
self.targetDB = SQLTable('test.sqltable_join2',
dropIfExists=True, createTable="""\
CREATE TABLE test.sqltable_join2 (third_id INTEGER PRIMARY KEY,
other_id VARCHAR(16))
""")
self.db.cursor.execute("""\
INSERT INTO test.sqltable_join1 VALUES (2,'seq2')
""")
self.db.cursor.execute("""\
INSERT INTO test.sqltable_join1 VALUES (3,'seq3')
""")
self.db.cursor.execute("""\
INSERT INTO test.sqltable_join1 VALUES (4,'seq4')
""")
self.db.cursor.execute("""\
INSERT INTO test.sqltable_join2 VALUES (7, 'seq2')
""")
self.db.cursor.execute("""\
INSERT INTO test.sqltable_join2 VALUES (99, 'seq3')
""")
self.db.cursor.execute("""\
INSERT INTO test.sqltable_join2 VALUES (6, 'seq4')
""")
self.db.cursor.execute("""\
INSERT INTO test.sqltable_join2 VALUES (8, 'seq4')
""")
suites = map(loader, tests)
return unittest.TestSuite(suites)
def mysql_enabled():
"""
Detects whether mysql is functional on the current system
"""
try:
import MySQLdb
except ImportError, exc:
msg = 'MySQLdb error: %s' % exc
warn(msg)
return False
try:
from pygr import sqlgraph
tempcurs = sqlgraph.getNameCursor()[1]
# disable some MySQL specific spurious warnings, current scope only
warnings.simplefilter("ignore")
tempcurs.execute('create database if not exists test')
except Exception, exc:
msg = 'cannot operate on MySql database: %s' % exc
warn(msg)
return False
return True
def sqlite_enabled():
"""
Detects whether sqlite3 is functional on the current system
"""