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import sqlalchemy as sql
from cogent.util import table as cogent_table
from cogent.db.ensembl.host import DbConnection, get_db_name
from cogent.util.misc import flatten
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley", "Jason Merkin"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "alpha"
class Database(object):
"""holds the data-base connection and table attributes"""
def __init__(self, account, species=None, db_type=None, release=None,
pool_recycle=None, division=None):
self._tables = {}
self.db_name = get_db_name(account=account, species=species,
release=release, db_type=db_type, division=division)
if not self.db_name:
raise RuntimeError, "%s db doesn't exist for '%s' on '%s'" % \
(db_type, species, account.host)
else:
self.db_name = self.db_name[0]
self._db = DbConnection(account=account, db_name=self.db_name,
pool_recycle=pool_recycle)
self._meta = sql.MetaData(self._db)
self.Type = db_type
def __str__(self):
return str(self.db_name)
def __cmp__(self, other):
return cmp(self._db, other._db)
def getTable(self, name):
"""returns the SQLalchemy table instance"""
table = self._tables.get(name, None)
if table is None:
c = self._db.execute("DESCRIBE %s" % name)
custom_columns = []
for r in c.fetchall():
Field = r["Field"]
Type = r["Type"]
if "tinyint" in Type:
custom_columns.append(sql.Column(Field, sql.Integer))
try:
table = sql.Table(name, self._meta, autoload=True,
extend_existing=True, *custom_columns)
except TypeError:
# new arg name not supported, try old
table = sql.Table(name, self._meta, autoload=True,
useexisting=True, *custom_columns)
self._tables[name] = table
return table
def getDistinct(self, table_name, column):
"""returns the Ensembl data-bases distinct values for the named
property_type.
Arguments:
- table_name: the data base table name
- column: valid values are biotype, status"""
table = self.getTable(table_name)
query = sql.select([table.c[column]], distinct=True)
records = set()
string_types = str, unicode
for record in query.execute():
if type(record) not in string_types and \
type(record[0]) not in string_types:
# multi-dimensioned list/tuple
record = flatten(record)
elif type(record) not in string_types:
# list/tuple of strings
record = tuple(record)
else:
# a string
record = [record]
records.update(record)
return records
def tableHasColumn(self, table_name, column):
"""returns True if table has column"""
table = self.getTable(table_name)
return hasattr(table.c, column)
def getTablesRowCount(self, table_name=None):
"""returns a cogent Table object with the row count for each table
in the database
Arguments:
- table_name: database table name. If none, all database tables
assessed."""
if type(table_name) == str:
table_name = (table_name,)
elif table_name is None:
self._meta.reflect()
table_name = self._meta.tables.keys()
rows = []
for name in table_name:
table = self.getTable(name)
count = table.count().execute().fetchone()[0]
rows.append(['%s.%s' % (self.db_name, name), count])
return cogent_table.Table(header=['name', 'count'], rows=rows)
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