def __init__(self, **kwargs):
self.db = None
try:
self.dbfact = DatabaseFactory(**kwargs)
self.database = self.dbfact.get_database()
self.db = db
self.db.initialize(self.database)
self.db.connect()
except (AttributeError, PeeweeException) as err:
fatal("Can't create database object: %s" % str(err))
def check_table_exists(cls, table):
"""Check a table exists in the database
Args:
table (:obj:`str`): Database `table` name to check.
Returns:
True
Raises:
SystemExit: if `table` does not exist
"""
if not table.table_exists():
fatal("Table %s does not exist" % (str(table.get_table_name())))
return True
def check_list_ids(ids):
"""Check the list of ids is not longer that MAX_LIST
Args:
ids (:obj:`list`): List of bind values
Returns:
True
Raises:
SystemExit: If `len` of the list of greater than `MAX_LIST`.
"""
if len(ids) > TaxaDB.MAX_LIST:
fatal("Too many accession entries to request (%d), max %d" %
(len(ids), TaxaDB.MAX_LIST))
return True
def set_accession_file(self, acc_file):
"""Set the accession file to use
Args:
acc_file (:obj:`str`): File to be set
Returns:
True
Raises:
SystemExit: If `acc_file` is None or not a file (`check_file`)
"""
if acc_file is None:
fatal("Please provide an accession file to set")
self.check_file(acc_file)
self.acc_file = acc_file
return True
def set_names_file(self, names_file):
"""Set names_file
Set the accession file to use
Args:
names_file (:obj:`str`): Nodes file to be set
Returns:
True
Raises:
SystemExit: If `names_file` is None or not a file (`check_file`)
"""
if names_file is None:
fatal("Please provide an names file to set")
self.check_file(names_file)
self.names_file = names_file
return True
def check_file(element):
"""Make some check on a file
This method is used to check an `element` is a real file.
Args:
element (:obj:`type`): File to check
Returns:
True
Raises:
SystemExit: if `element` file does not exist
SystemExit: if `element` is not a file
"""
if element is None:
fatal("Please provide an input file to check")
if not os.path.exists(element):
fatal("File %s does not exist" % str(element))
if not os.path.isfile(element):
fatal("%s is not a file" % str(element))
return True
def test_fatal_throws(self):
"""Check fatal throws SystemExit"""
with self.assertRaises(SystemExit):
fatal("failed")