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def close(self):
if self.closed:
return
self.db.close()
if self.flags & db.DB_RDONLY == 0:
self.unlock()
self.closed = True
LOG.warning("Error closing db environment for '%s': %s" %
(name, str(msg)))
return "Unknown", bsddb_version, "Unknown"
dbmap1 = dbshelve.DBShelf(env)
fname = os.path.join(dirpath, META + ".db")
try:
dbmap1.open(fname, META, db.DB_HASH, db.DB_RDONLY)
except:
env.close()
return "Unknown", bsddb_version, "Unknown"
schema_version = dbmap1.get(b'version', default=None)
dbmap1.close()
dbmap2 = dbshelve.DBShelf(env)
fname = os.path.join(dirpath, PERSON_TBL + ".db")
try:
dbmap2.open(fname, PERSON_TBL, db.DB_HASH, db.DB_RDONLY)
except:
env.close()
return "Unknown", bsddb_version, schema_version
count = len(dbmap2)
dbmap2.close()
env.close()
return (count, bsddb_version, schema_version)
db.DB_INIT_LOG | db.DB_INIT_TXN
try:
env.open(dirpath, flags)
except Exception as msg:
LOG.warning("Error opening db environment for '%s': %s" %
(name, str(msg)))
try:
env.close()
except Exception as msg:
LOG.warning("Error closing db environment for '%s': %s" %
(name, str(msg)))
return "Unknown", bsddb_version, "Unknown"
dbmap1 = dbshelve.DBShelf(env)
fname = os.path.join(dirpath, META + ".db")
try:
dbmap1.open(fname, META, db.DB_HASH, db.DB_RDONLY)
except:
env.close()
return "Unknown", bsddb_version, "Unknown"
schema_version = dbmap1.get(b'version', default=None)
dbmap1.close()
dbmap2 = dbshelve.DBShelf(env)
fname = os.path.join(dirpath, PERSON_TBL + ".db")
try:
dbmap2.open(fname, PERSON_TBL, db.DB_HASH, db.DB_RDONLY)
except:
env.close()
return "Unknown", bsddb_version, schema_version
count = len(dbmap2)
dbmap2.close()
env.close()
return (count, bsddb_version, schema_version)
def open(self, filename, dbname, filetype, flags=db.DB_CREATE, mode=0644):
self.filename = filename
self.closed = False
if type(flags) == type(''):
sflag = flags
if sflag == 'r':
flags = db.DB_RDONLY
elif sflag == 'rw':
flags = 0
elif sflag == 'w':
flags = db.DB_CREATE
elif sflag == 'c':
flags = db.DB_CREATE
elif sflag == 'n':
flags = db.DB_TRUNCATE | db.DB_CREATE
else:
raise Error, _("Flags should be one of 'r', 'w', 'c' or 'n' or use the bsddb.db.DB_* flags")
self.flags = flags
if self.flags & db.DB_RDONLY == 0:
flags |= db.DB_AUTO_COMMIT # use txn subsystem in write mode
self.lock()
filename = os.path.realpath(filename) # we give absolute path due to dbenv
#print 'opening', filename, filetype, flags, mode
if type(flags) == type(''):
sflag = flags
if sflag == 'r':
flags = db.DB_RDONLY
elif sflag == 'rw':
flags = 0
elif sflag == 'w':
flags = db.DB_CREATE
elif sflag == 'c':
flags = db.DB_CREATE
elif sflag == 'n':
flags = db.DB_TRUNCATE | db.DB_CREATE
else:
raise Error, _("Flags should be one of 'r', 'w', 'c' or 'n' or use the bsddb.db.DB_* flags")
self.flags = flags
if self.flags & db.DB_RDONLY == 0:
flags |= db.DB_AUTO_COMMIT # use txn subsystem in write mode
self.lock()
filename = os.path.realpath(filename) # we give absolute path due to dbenv
#print 'opening', filename, filetype, flags, mode
return self.db.open(filename, None, filetype, flags, mode)
def convert_index(infile, config, num_samples):
in_graph = db.DB()
in_graph.set_cachesize(4,0)
in_graph.open(infile+"/graph", flags=db.DB_RDONLY)
# Create the kmer signature index
storage=get_storage(config)
storage.set_integer(BLOOMFILTER_SIZE_KEY, config["m"])
storage.set_integer(NUM_HASH_FUNCTS_KEY, config["h"])
BitMatrix.create(storage=storage,
rows=get_rows(in_graph, config["m"]), num_rows=config["m"], num_cols=num_samples)
in_graph.close()
def __init__(self, dbname, mode = "r"):
if mode not in ("r", "rw"):
raise TypeError("Unknown mode: %r" % (mode,))
self.__need_flush = 0
BaseDB.OpenDB.__init__(self, dbname, INDEX_TYPE)
self.dbenv = None
dbenv = db.DBEnv()
envflags = db.DB_THREAD | db.DB_INIT_MPOOL
dbenv.open(dbname, envflags)
if mode == "r":
self._dbopen_flags = db.DB_RDONLY
else:
self._dbopen_flags = 0
self.primary_table = db.DB(dbenv)
self.primary_table.open("key_%s" % (self.primary_namespace,),
None,
db.DB_BTREE, self._dbopen_flags, 0660)
self.secondary_tables = {}
self.dbenv = dbenv
def open(self, filename, dbname, filetype, flags=db.DB_CREATE, mode=0644):
self.filename = filename
self.closed = False
if type(flags) == type(''):
sflag = flags
if sflag == 'r':
flags = db.DB_RDONLY
elif sflag == 'rw':
flags = 0
elif sflag == 'w':
flags = db.DB_CREATE
elif sflag == 'c':
flags = db.DB_CREATE
elif sflag == 'n':
flags = db.DB_TRUNCATE | db.DB_CREATE
else:
raise Error, _("Flags should be one of 'r', 'w', 'c' or 'n' or use the bsddb.db.DB_* flags")
self.flags = flags
if self.flags & db.DB_RDONLY == 0:
flags |= db.DB_AUTO_COMMIT # use txn subsystem in write mode
self.lock()
filename = os.path.realpath(filename) # we give absolute path due to dbenv
#print 'opening', filename, filetype, flags, mode