class SQLTable_Setup(unittest.TestCase):
tableClass = SQLTable
def __init__(self, *args, **kwargs):
unittest.TestCase.__init__(self, *args, **kwargs)
self.serverInfo = DBServerInfo() # share conn for all tests
def setUp(self):
try:
self.load_data(writeable=self.writeable)
except ImportError:
raise SkipTest('missing MySQLdb module?')
def load_data(self, tableName='test.sqltable_test', writeable=False):
'create 3 tables and load 9 rows for our tests'
self.tableName = tableName
self.joinTable1 = joinTable1 = tableName + '1'
self.joinTable2 = joinTable2 = tableName + '2'
createTable = """\
CREATE TABLE %s (primary_id INTEGER PRIMARY KEY %%(AUTO_INCREMENT)s, seq_id TEXT, start INTEGER, stop INTEGER)
""" % tableName
self.db = self.tableClass(tableName, dropIfExists=True,
serverInfo=self.serverInfo,
createTable=createTable,
writeable=writeable)
self.sourceDB = self.tableClass(joinTable1, serverInfo=self.serverInfo,
dropIfExists=True, createTable="""\
CREATE TABLE %s (my_id INTEGER PRIMARY KEY,
other_id VARCHAR(16))
""" % joinTable1)
self.targetDB = self.tableClass(joinTable2, serverInfo=self.serverInfo,
dropIfExists=True, createTable="""\
CREATE TABLE %s (third_id INTEGER PRIMARY KEY,
other_id VARCHAR(16))
""" % joinTable2)
sql = """
INSERT INTO %s (seq_id, start, stop) VALUES ('seq1', 0, 10)
INSERT INTO %s (seq_id, start, stop) VALUES ('seq2', 5, 15)
INSERT INTO %s VALUES (2,'seq2')
INSERT INTO %s VALUES (3,'seq3')
INSERT INTO %s VALUES (4,'seq4')
INSERT INTO %s VALUES (7, 'seq2')
INSERT INTO %s VALUES (99, 'seq3')
INSERT INTO %s VALUES (6, 'seq4')
INSERT INTO %s VALUES (8, 'seq4')
""" % tuple(([tableName]*2) + ([joinTable1]*3) + ([joinTable2]*4))
for line in sql.strip().splitlines(): # insert our test data
self.db.cursor.execute(line.strip())
def tearDown(self):
self.db.cursor.execute('drop table if exists %s' % self.tableName)
self.db.cursor.execute('drop table if exists %s' % self.joinTable1)
self.db.cursor.execute('drop table if exists %s' % self.joinTable2)
self.serverInfo.close()
def setUp(self):
# test will be skipped if mysql module or ensembldb server unavailable
logger.debug('accessing ensembldb.ensembl.org')
conn = DBServerInfo(host='ensembldb.ensembl.org',
user='******',
passwd='')
try:
translationDB = \
SQLTableCatcher('homo_sapiens_core_47_36i.translation',
serverInfo=conn)
translationDB.catchIter = True # should not iter in this test!
exonDB = SQLTable('homo_sapiens_core_47_36i.exon', serverInfo=conn)
except ImportError, e:
raise SkipTest(e)
def __init__(self, *args, **kwargs):
unittest.TestCase.__init__(self, *args, **kwargs)
self.serverInfo = DBServerInfo() # share conn for all tests
class SQLTable_Setup(unittest.TestCase):
tableClass = SQLTableCatcher
serverArgs = {}
loadArgs = {}
def __init__(self, *args, **kwargs):
unittest.TestCase.__init__(self, *args, **kwargs)
# share conn for all tests
self.serverInfo = DBServerInfo(** self.serverArgs)
def setUp(self):
if not testutil.mysql_enabled():
raise SkipTest("no MySQL installed")
self.load_data(writeable=self.writeable, ** self.loadArgs)
def load_data(self, tableName='test.sqltable_test', writeable=False,
dbargs={}, sourceDBargs={}, targetDBargs={}):
'create 3 tables and load 9 rows for our tests'
self.tableName = tableName
self.joinTable1 = joinTable1 = tableName + '1'
self.joinTable2 = joinTable2 = tableName + '2'
createTable = 'CREATE TABLE %s (primary_id INTEGER PRIMARY KEY \
%%(AUTO_INCREMENT)s, seq_id TEXT, start INTEGER, \
stop INTEGER)' % tableName
self.db = self.tableClass(tableName, dropIfExists=True,
serverInfo=self.serverInfo,
createTable=createTable,
writeable=writeable,
attrAlias=dict(sequence_id='seq_id',
minStop="min(stop)"),
**dbargs)
self.sourceDB = self.tableClass(joinTable1, serverInfo=self.serverInfo,
dropIfExists=True, createTable="""\
CREATE TABLE %s (my_id INTEGER PRIMARY KEY,
other_id VARCHAR(16))
""" % joinTable1, **sourceDBargs)
self.targetDB = self.tableClass(joinTable2, serverInfo=self.serverInfo,
dropIfExists=True, createTable="""\
CREATE TABLE %s (third_id INTEGER PRIMARY KEY,
other_id VARCHAR(16))
""" % joinTable2, **targetDBargs)
sql = """
INSERT INTO %s (seq_id, start, stop) VALUES ('seq1', 0, 10)
INSERT INTO %s (seq_id, start, stop) VALUES ('seq2', 5, 15)
INSERT INTO %s VALUES (2,'seq2')
INSERT INTO %s VALUES (3,'seq3')
INSERT INTO %s VALUES (4,'seq4')
INSERT INTO %s VALUES (7, 'seq2')
INSERT INTO %s VALUES (99, 'seq3')
INSERT INTO %s VALUES (6, 'seq4')
INSERT INTO %s VALUES (8, 'seq4')
""" % tuple(([tableName]*2) + ([joinTable1]*3) + ([joinTable2]*4))
for line in sql.strip().splitlines(): # insert our test data
self.db.cursor.execute(line.strip())
# Another table, for the "ORDER BY" test
self.orderTable = tableName + '_orderBy'
self.db.cursor.execute('DROP TABLE IF EXISTS %s' % self.orderTable)
self.db.cursor.execute('CREATE TABLE %s (id INTEGER PRIMARY KEY, \
number INTEGER, letter VARCHAR(1))'
% self.orderTable)
for row in range(0, 10):
self.db.cursor.execute('INSERT INTO %s VALUES (%d, %d, \'%s\')' %
(self.orderTable, row,
random.randint(0, 99),
string.lowercase[random.randint(0,
len(string.lowercase)
- 1)]))
def tearDown(self):
self.db.cursor.execute('drop table if exists %s' % self.tableName)
self.db.cursor.execute('drop table if exists %s' % self.joinTable1)
self.db.cursor.execute('drop table if exists %s' % self.joinTable2)
self.db.cursor.execute('drop table if exists %s' % self.orderTable)
self.serverInfo.close()
def __init__(self, *args, **kwargs):
unittest.TestCase.__init__(self, *args, **kwargs)
# share conn for all tests
self.serverInfo = DBServerInfo(**self.serverArgs)
class SQLTable_Setup(unittest.TestCase):
tableClass = SQLTableCatcher
serverArgs = {}
loadArgs = {}
def __init__(self, *args, **kwargs):
unittest.TestCase.__init__(self, *args, **kwargs)
# share conn for all tests
self.serverInfo = DBServerInfo(**self.serverArgs)
def setUp(self):
if not testutil.mysql_enabled():
raise SkipTest("no MySQL installed")
self.load_data(writeable=self.writeable, **self.loadArgs)
def load_data(self,
tableName='test.sqltable_test',
writeable=False,
dbargs={},
sourceDBargs={},
targetDBargs={}):
'create 3 tables and load 9 rows for our tests'
self.tableName = tableName
self.joinTable1 = joinTable1 = tableName + '1'
self.joinTable2 = joinTable2 = tableName + '2'
createTable = 'CREATE TABLE %s (primary_id INTEGER PRIMARY KEY \
%%(AUTO_INCREMENT)s, seq_id TEXT, start INTEGER, \
stop INTEGER)' % tableName
self.db = self.tableClass(tableName,
dropIfExists=True,
serverInfo=self.serverInfo,
createTable=createTable,
writeable=writeable,
attrAlias=dict(sequence_id='seq_id',
minStop="min(stop)"),
**dbargs)
self.sourceDB = self.tableClass(joinTable1,
serverInfo=self.serverInfo,
dropIfExists=True,
createTable="""\
CREATE TABLE %s (my_id INTEGER PRIMARY KEY,
other_id VARCHAR(16))
""" % joinTable1,
**sourceDBargs)
self.targetDB = self.tableClass(joinTable2,
serverInfo=self.serverInfo,
dropIfExists=True,
createTable="""\
CREATE TABLE %s (third_id INTEGER PRIMARY KEY,
other_id VARCHAR(16))
""" % joinTable2,
**targetDBargs)
sql = """
INSERT INTO %s (seq_id, start, stop) VALUES ('seq1', 0, 10)
INSERT INTO %s (seq_id, start, stop) VALUES ('seq2', 5, 15)
INSERT INTO %s VALUES (2,'seq2')
INSERT INTO %s VALUES (3,'seq3')
INSERT INTO %s VALUES (4,'seq4')
INSERT INTO %s VALUES (7, 'seq2')
INSERT INTO %s VALUES (99, 'seq3')
INSERT INTO %s VALUES (6, 'seq4')
INSERT INTO %s VALUES (8, 'seq4')
""" % tuple(([tableName] * 2) + ([joinTable1] * 3) +
([joinTable2] * 4))
for line in sql.strip().splitlines(): # insert our test data
self.db.cursor.execute(line.strip())
# Another table, for the "ORDER BY" test
self.orderTable = tableName + '_orderBy'
self.db.cursor.execute('DROP TABLE IF EXISTS %s' % self.orderTable)
self.db.cursor.execute('CREATE TABLE %s (id INTEGER PRIMARY KEY, \
number INTEGER, letter VARCHAR(1))' %
self.orderTable)
for row in range(0, 10):
self.db.cursor.execute(
'INSERT INTO %s VALUES (%d, %d, \'%s\')' %
(self.orderTable, row, random.randint(0, 99),
string.lowercase[random.randint(0,
len(string.lowercase) - 1)]))
def tearDown(self):
self.db.cursor.execute('drop table if exists %s' % self.tableName)
self.db.cursor.execute('drop table if exists %s' % self.joinTable1)
self.db.cursor.execute('drop table if exists %s' % self.joinTable2)
self.db.cursor.execute('drop table if exists %s' % self.orderTable)
self.serverInfo.close()