def setUp(self):
self.tmpfile = tempfile.mktemp(dir=self.work_dir)
self.db = TrajectoryInfoCache(self.tmpfile)
assert len(self.db._database) == 1, len(self.db._database)
assert 'db_version' in self.db._database
assert int(self.db._database['db_version']) >= 1
def test_no_sqlite(self):
# create new instance (init has to be called, install temporary import hook to raise importerror for sqlite3
import sys
del sys.modules['sqlite3']
class meta_ldr(object):
def find_module(self, fullname, path):
if fullname.startswith('sqlite3'):
return self
def load_module(self, fullname, path=None):
raise ImportError()
import warnings
try:
sys.meta_path.insert(0, meta_ldr())
# import sqlite3
with warnings.catch_warnings(record=True) as cw:
db = TrajectoryInfoCache()
self.assertNotIsInstance(db._database, SqliteDB)
self.assertEqual(len(cw), 1)
self.assertIn("sqlite3 package not available",
cw[0].message.args[0])
finally:
del sys.meta_path[0]
def setUp(self):
self.work_dir = tempfile.mkdtemp("traj_cache_test")
self.tmpfile = tempfile.mktemp(dir=self.work_dir)
self.db = TrajectoryInfoCache(self.tmpfile)
# overwrite TrajectoryInfoCache._instance with self.db...
TrajectoryInfoCache._instance = self.db
def setUp(self):
self.work_dir = tempfile.mkdtemp(prefix="traj_cache_test")
self.tmpfile = tempfile.mktemp(dir=self.work_dir)
self.db = TrajectoryInfoCache(self.tmpfile)
# overwrite TrajectoryInfoCache._instance with self.db...
TrajectoryInfoCache._instance = self.db
config.use_trajectory_lengths_cache = True
def test_corrupted_db(self):
with NamedTemporaryFile(mode='w', suffix='.dat', delete=False) as f:
f.write("makes no sense!!!!")
f.close()
name = f.name
db = TrajectoryInfoCache(name)
# ensure we can perform lookups on the broken db without exception.
r = api.source(xtcfiles[0], top=pdbfile)
db[xtcfiles[0], r]
def test_no_sqlite(self):
def import_mock(name, *args):
if name == 'sqlite3':
raise ImportError("we pretend not to have this")
return __import__(name, *args)
from pyemma.coordinates.data.util import traj_info_cache
with mock.patch('pyemma.coordinates.data.util.traj_info_cache',
'__import__',
side_effect=import_mock,
create=True):
TrajectoryInfoCache._instance = None
TrajectoryInfoCache(self.tempfile)
def test_corrupted_db(self):
with NamedTemporaryFile(mode='w', suffix='.dat', delete=False) as f:
f.write("makes no sense!!!!")
f.close()
name = f.name
import warnings
with warnings.catch_warnings(record=True) as cm:
warnings.simplefilter('always')
db = TrajectoryInfoCache(name)
assert len(cm) == 1
assert "corrupted" in str(cm[-1].message)
# ensure we can perform lookups on the broken db without exception.
r = api.source(xtcfiles[0], top=pdbfile)
db[xtcfiles[0], r]
def test_old_db_conversion(self):
# prior 2.1, database only contained lengths (int as string) entries
# check conversion is happening
with NamedTemporaryFile(suffix='.npy', delete=False) as f:
db = TrajectoryInfoCache(None)
fn = f.name
np.save(fn, [1, 2, 3])
f.close() # windows sucks
reader = api.source(fn)
hash = db._get_file_hash(fn)
db._database = {hash: str(3)}
info = db[fn, reader]
assert info.length == 3
assert info.ndim == 1
assert info.offsets == []
def test_old_db_conversion(self):
# prior 2.1, database only contained lengths (int as string) entries
# check conversion is happening
with NamedTemporaryFile(suffix='.npy', delete=False) as f:
db = TrajectoryInfoCache(None)
fn = f.name
np.save(fn, [1, 2, 3])
f.close() # windows sucks
reader = api.source(fn)
hash = db._get_file_hash(fn)
from pyemma.coordinates.data.util.traj_info_backends import DictDB
db._database = DictDB()
db._database.db_version = 0
info = db[fn, reader]
assert info.length == 3
assert info.ndim == 1
assert info.offsets == []
def test_in_memory_db(self):
""" new instance, not yet saved to disk, no lru cache avail """
old_cfg_dir = config.cfg_dir
try:
config._cfg_dir = ''
db = TrajectoryInfoCache()
reader = pyemma.coordinates.source(xtcfiles, top=pdbfile)
info = db[xtcfiles[0], reader]
self.assertIsInstance(db._database, SqliteDB)
directory = db._database._database_from_key(info.hash_value)
assert directory is None
finally:
from pyemma.util.exceptions import ConfigDirectoryException
try:
config.cfg_dir = old_cfg_dir
except ConfigDirectoryException:
pass