def test_xmippWriteImages(self):
projName = "relion_ribo"
project = self.loadProject(projName) # Now it will be loaded if exists
sets = project.mapper.selectByClass('SetOfParticles')
print sets[0]
# print "writing set to .xmd"
# from pyworkflow.em.packages.xmipp3 import writeSetOfParticles
#
# writeSetOfParticles(sets[0], "images.xmd")
print "iterating set:"
s = sets[0]
dbFn = s.getFileName()
print "FileName: ", dbFn
from sqlite3 import dbapi2 as sqlite
conn = sqlite.Connection(dbFn, check_same_thread = False)
conn.row_factory = sqlite.Row
cur = conn.cursor()
cur.execute('select * from Objects;')
#conn2 = sqlite.Connection(':memory:')
#cur2 = conn2.cursor()
i = 0
# for line in conn.iterdump():
row = cur.fetchone()
while row is not None:
#yield row
row = cur.fetchone()
#cur2.executescript(line)
i += 1
print "Total lines: ", i
print s.getObjDict()
def __init__(self, dbName=None):
if dbName is None:
dbName = getProgramsDbName()
self.dbName = dbName
from sqlite3 import dbapi2 as sqlite
self.connection = sqlite.Connection(dbName, timeout=self.DB_TIMEOUT)
self.connection.row_factory = sqlite.Row
self.cursor = self.connection.cursor()
self.cursor.execute('pragma foreign_keys=ON')
def _createConnection(self, dbName, timeout):
"""Establish db connection"""
self._dbName = dbName
if self._reuseConnections and dbName in self.OPEN_CONNECTIONS:
self.connection = self.OPEN_CONNECTIONS[dbName]
else:
self.connection = sqlite.Connection(dbName, timeout, check_same_thread=False)
self.connection.row_factory = sqlite.Row
self.OPEN_CONNECTIONS[dbName] = self.connection
self.cursor = self.connection.cursor()
# Define some shortcuts functions
if envVarOn(SCIPION_DEBUG_SQLITE):
self.executeCommand = self._debugExecute
else:
self.executeCommand = self.cursor.execute
self.commit = self.connection.commit
def main():
parser = ArgumentParser()
parser.add_argument('profile_paths',
nargs='*',
metavar='PATH',
help='Profiles to analyze (default: auto detection)')
parser.add_argument('--version',
action='version',
version='%(prog)s ' + VERSION_STR)
options = parser.parse_args()
if options.profile_paths:
profiles_to_scan = options.profile_paths
else:
profiles_to_scan = []
for pattern in (
os.path.expanduser('~/.mozilla/*/*.*/'),
os.path.expanduser('~/.thunderbird/*.*/'),
os.path.expanduser('~/.icedove/*.*/'),
):
profiles_to_scan += glob(pattern)
details_of_profile = {}
d = {
'version': 4,
'profiles': details_of_profile,
}
success = True
for profile_path in profiles_to_scan:
filename = os.path.join(profile_path, 'signons.sqlite')
if not os.path.exists(filename):
print('Database file "%s" not found' % filename, file=sys.stderr)
continue
try:
connection = sqlite.Connection(filename)
except sqlite.OperationalError as e:
print('%s (file "%s")' % (e, filename), file=sys.stderr)
continue
details_of_id = {}
details_of_profile[profile_path] = details_of_id
cursor = connection.execute('''
SELECT *
, "" AS decryptedUsername
, "" AS decryptedPassword
FROM moz_logins
''')
for password_entry in map(MozLogin._make, cursor.fetchall()):
for entryped_text, target_key in (
(password_entry.encryptedPassword, 'decryptedPassword'),
(password_entry.encryptedUsername, 'decryptedUsername'),
):
encrypted_text_encoded = entryped_text.encode('utf-8')
decrypted_text = None
try:
decrypted_text = \
decrypt_single(profile_path, encrypted_text_encoded)
except NssInitializationError:
print('NSS initialization failed for profile path "%s".' %
profile_path,
file=sys.stderr)
sys.exit(1)
except NssLinkingError as e:
print('Dynamically linking to NSS failed: %s' % e,
file=sys.stderr)
sys.exit(1)
except Base64DecodingError:
print('Base64 decoding failed (database "%s", id %d).' %
(filename, _id),
file=sys.stderr)
success = False
continue
except PasswordDecryptionError:
print(
'Password decryption failed (database "%s", id %d).' %
(filename, _id),
file=sys.stderr)
success = False
continue
if decrypted_text:
kvargs = {target_key: decrypted_text}
password_entry = password_entry._replace(**kvargs)
details_of_id[password_entry.id] = password_entry._asdict()
connection.close()
if d:
try:
json.dump(d, sys.stdout, indent=4, sort_keys=True)
print()
except IOError as e:
if e.errno != errno.EPIPE: # e.g. when hitting 'q' in less
raise
sys.exit(int(not success))
def _get_conn(self):
id = get_ident()
if id not in self._connection_cache:
self._connection_cache[id] = sqlite3.Connection(self.path,
timeout=60)
return self._connection_cache[id]
