def test_treestore(self):
output = convert(
'tree',
{'format': 'newick', 'data': self.newick},
{'format': 'r.apetree'})
output = convert('tree', output, {'format': 'treestore'})
self.assertEqual(output['format'], 'treestore')
rows = bson.decode_all(output['data'])
for d in rows:
if 'rooted' in d:
root = d
self.assertNotEqual(root, None)
self.assertEqual(len(root['clades']), 1)
def findId(id):
for d in rows:
if d['_id'] == id:
return d
top = findId(root['clades'][0])
self.assertEqual(len(top['clades']), 2)
internal = findId(top['clades'][0])
rubribarbus = findId(top['clades'][1])
ahli = findId(internal['clades'][0])
allogus = findId(internal['clades'][1])
self.assertEqual(internal['branch_length'], 2)
self.assertEqual(ahli['name'], 'ahli')
self.assertEqual(ahli['branch_length'], 0)
self.assertEqual(allogus['name'], 'allogus')
self.assertEqual(allogus['branch_length'], 1)
self.assertEqual(rubribarbus['name'], 'rubribarbus')
self.assertEqual(rubribarbus['branch_length'], 3)
python类decode_all()的实例源码
def push(data, spec, **kwargs):
import pymongo
import bson
db = spec['db']
collection = spec['collection']
host = spec.get('host', 'localhost')
bson_data = bson.decode_all(data)
c = pymongo.MongoClient(host)[db][collection]
# TODO is this really what we want? Dropping the whole collection?
# Seems dangerous, might be unexpected.
c.drop()
if len(bson_data) > 0:
c.insert(bson_data)
def load(self, load_one=False, filename=None):
f = None
if not filename:
filename = self.state_file
try:
f = open(filename, "r")
data = decode_all(f.read())
if load_one and len(data) > 0:
return data[0]
return data
except Exception, e:
raise e
finally:
if f:
f.close()
def _unpack_response(response, cursor_id=None, codec_options=CodecOptions()):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
Can raise CursorNotFound, NotMasterError, ExecutionTimeout, or
OperationFailure.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `codec_options` (optional): an instance of
:class:`~bson.codec_options.CodecOptions`
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
assert cursor_id is not None
# Fake a getMore command response. OP_GET_MORE provides no document.
msg = "Cursor not found, cursor id: %d" % (cursor_id,)
errobj = {"ok": 0, "errmsg": msg, "code": 43}
raise CursorNotFound(msg, 43, errobj)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
# Fake the ok field if it doesn't exist.
error_object.setdefault("ok", 0)
if error_object["$err"].startswith("not master"):
raise NotMasterError(error_object["$err"], error_object)
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {"cursor_id": struct.unpack("<q", response[4:12])[0],
"starting_from": struct.unpack("<i", response[12:16])[0],
"number_returned": struct.unpack("<i", response[16:20])[0],
"data": bson.decode_all(response[20:], codec_options)}
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response, cursor_id=None, as_class=dict,
tz_aware=False, uuid_subtype=OLD_UUID_SUBTYPE,
compile_re=True):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `as_class` (optional): class to use for resulting documents
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
assert cursor_id is not None
raise CursorNotFound("cursor id '%s' not valid at server" %
cursor_id)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
if error_object["$err"].startswith("not master"):
raise AutoReconnect(error_object["$err"])
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {}
result["cursor_id"] = struct.unpack("<q", response[4:12])[0]
result["starting_from"] = struct.unpack("<i", response[12:16])[0]
result["number_returned"] = struct.unpack("<i", response[16:20])[0]
result["data"] = bson.decode_all(response[20:],
as_class, tz_aware, uuid_subtype,
compile_re)
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response, cursor_id=None, as_class=dict,
tz_aware=False, uuid_subtype=OLD_UUID_SUBTYPE,
compile_re=True):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `as_class` (optional): class to use for resulting documents
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
assert cursor_id is not None
raise CursorNotFound("cursor id '%s' not valid at server" %
cursor_id)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
if error_object["$err"].startswith("not master"):
raise AutoReconnect(error_object["$err"])
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {}
result["cursor_id"] = struct.unpack("<q", response[4:12])[0]
result["starting_from"] = struct.unpack("<i", response[12:16])[0]
result["number_returned"] = struct.unpack("<i", response[16:20])[0]
result["data"] = bson.decode_all(response[20:],
as_class, tz_aware, uuid_subtype,
compile_re)
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response, cursor_id=None, as_class=dict,
tz_aware=False, uuid_subtype=OLD_UUID_SUBTYPE,
compile_re=True):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `as_class` (optional): class to use for resulting documents
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
assert cursor_id is not None
raise CursorNotFound("cursor id '%s' not valid at server" %
cursor_id)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
if error_object["$err"].startswith("not master"):
raise AutoReconnect(error_object["$err"])
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {}
result["cursor_id"] = struct.unpack("<q", response[4:12])[0]
result["starting_from"] = struct.unpack("<i", response[12:16])[0]
result["number_returned"] = struct.unpack("<i", response[16:20])[0]
result["data"] = bson.decode_all(response[20:],
as_class, tz_aware, uuid_subtype,
compile_re)
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response, cursor_id=None, as_class=dict,
tz_aware=False, uuid_subtype=OLD_UUID_SUBTYPE,
compile_re=True):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `as_class` (optional): class to use for resulting documents
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
assert cursor_id is not None
raise CursorNotFound("cursor id '%s' not valid at server" %
cursor_id)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
if error_object["$err"].startswith("not master"):
raise AutoReconnect(error_object["$err"])
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {}
result["cursor_id"] = struct.unpack("<q", response[4:12])[0]
result["starting_from"] = struct.unpack("<i", response[12:16])[0]
result["number_returned"] = struct.unpack("<i", response[16:20])[0]
result["data"] = bson.decode_all(response[20:],
as_class, tz_aware, uuid_subtype,
compile_re)
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response,
cursor_id=None,
codec_options=_UNICODE_REPLACE_CODEC_OPTIONS):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
Can raise CursorNotFound, NotMasterError, ExecutionTimeout, or
OperationFailure.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `codec_options` (optional): an instance of
:class:`~bson.codec_options.CodecOptions`
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
if cursor_id is None:
raise ProtocolError("No cursor id for getMore operation")
# Fake a getMore command response. OP_GET_MORE provides no document.
msg = "Cursor not found, cursor id: %d" % (cursor_id,)
errobj = {"ok": 0, "errmsg": msg, "code": 43}
raise CursorNotFound(msg, 43, errobj)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
# Fake the ok field if it doesn't exist.
error_object.setdefault("ok", 0)
if error_object["$err"].startswith("not master"):
raise NotMasterError(error_object["$err"], error_object)
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {"cursor_id": struct.unpack("<q", response[4:12])[0],
"starting_from": struct.unpack("<i", response[12:16])[0],
"number_returned": struct.unpack("<i", response[16:20])[0],
"data": bson.decode_all(response[20:], codec_options)}
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response, cursor_id=None, as_class=dict,
tz_aware=False, uuid_subtype=OLD_UUID_SUBTYPE,
compile_re=True):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `as_class` (optional): class to use for resulting documents
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
assert cursor_id is not None
raise CursorNotFound("cursor id '%s' not valid at server" %
cursor_id)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
if error_object["$err"].startswith("not master"):
raise AutoReconnect(error_object["$err"])
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {}
result["cursor_id"] = struct.unpack("<q", response[4:12])[0]
result["starting_from"] = struct.unpack("<i", response[12:16])[0]
result["number_returned"] = struct.unpack("<i", response[16:20])[0]
result["data"] = bson.decode_all(response[20:],
as_class, tz_aware, uuid_subtype,
compile_re)
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response, cursor_id=None, codec_options=CodecOptions()):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
Can raise CursorNotFound, NotMasterError, ExecutionTimeout, or
OperationFailure.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `codec_options` (optional): an instance of
:class:`~bson.codec_options.CodecOptions`
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
assert cursor_id is not None
# Fake a getMore command response. OP_GET_MORE provides no document.
msg = "Cursor not found, cursor id: %d" % (cursor_id,)
errobj = {"ok": 0, "errmsg": msg, "code": 43}
raise CursorNotFound(msg, 43, errobj)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
# Fake the ok field if it doesn't exist.
error_object.setdefault("ok", 0)
if error_object["$err"].startswith("not master"):
raise NotMasterError(error_object["$err"], error_object)
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {"cursor_id": struct.unpack("<q", response[4:12])[0],
"starting_from": struct.unpack("<i", response[12:16])[0],
"number_returned": struct.unpack("<i", response[16:20])[0],
"data": bson.decode_all(response[20:], codec_options)}
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response,
cursor_id=None,
codec_options=_UNICODE_REPLACE_CODEC_OPTIONS):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
Can raise CursorNotFound, NotMasterError, ExecutionTimeout, or
OperationFailure.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `codec_options` (optional): an instance of
:class:`~bson.codec_options.CodecOptions`
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
if cursor_id is None:
raise ProtocolError("No cursor id for getMore operation")
# Fake a getMore command response. OP_GET_MORE provides no document.
msg = "Cursor not found, cursor id: %d" % (cursor_id,)
errobj = {"ok": 0, "errmsg": msg, "code": 43}
raise CursorNotFound(msg, 43, errobj)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
# Fake the ok field if it doesn't exist.
error_object.setdefault("ok", 0)
if error_object["$err"].startswith("not master"):
raise NotMasterError(error_object["$err"], error_object)
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {"cursor_id": struct.unpack("<q", response[4:12])[0],
"starting_from": struct.unpack("<i", response[12:16])[0],
"number_returned": struct.unpack("<i", response[16:20])[0],
"data": bson.decode_all(response[20:], codec_options)}
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response, cursor_id=None, codec_options=CodecOptions()):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
Can raise CursorNotFound, NotMasterError, ExecutionTimeout, or
OperationFailure.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `codec_options` (optional): an instance of
:class:`~bson.codec_options.CodecOptions`
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
assert cursor_id is not None
# Fake a getMore command response. OP_GET_MORE provides no document.
msg = "Cursor not found, cursor id: %d" % (cursor_id,)
errobj = {"ok": 0, "errmsg": msg, "code": 43}
raise CursorNotFound(msg, 43, errobj)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
# Fake the ok field if it doesn't exist.
error_object.setdefault("ok", 0)
if error_object["$err"].startswith("not master"):
raise NotMasterError(error_object["$err"], error_object)
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {"cursor_id": struct.unpack("<q", response[4:12])[0],
"starting_from": struct.unpack("<i", response[12:16])[0],
"number_returned": struct.unpack("<i", response[16:20])[0],
"data": bson.decode_all(response[20:], codec_options)}
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response, cursor_id=None, codec_options=CodecOptions()):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
Can raise CursorNotFound, NotMasterError, ExecutionTimeout, or
OperationFailure.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `codec_options` (optional): an instance of
:class:`~bson.codec_options.CodecOptions`
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
assert cursor_id is not None
# Fake a getMore command response. OP_GET_MORE provides no document.
msg = "Cursor not found, cursor id: %d" % (cursor_id,)
errobj = {"ok": 0, "errmsg": msg, "code": 43}
raise CursorNotFound(msg, 43, errobj)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
# Fake the ok field if it doesn't exist.
error_object.setdefault("ok", 0)
if error_object["$err"].startswith("not master"):
raise NotMasterError(error_object["$err"], error_object)
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {"cursor_id": struct.unpack("<q", response[4:12])[0],
"starting_from": struct.unpack("<i", response[12:16])[0],
"number_returned": struct.unpack("<i", response[16:20])[0],
"data": bson.decode_all(response[20:], codec_options)}
assert len(result["data"]) == result["number_returned"]
return result
def _unpack_response(response, cursor_id=None, codec_options=CodecOptions()):
"""Unpack a response from the database.
Check the response for errors and unpack, returning a dictionary
containing the response data.
Can raise CursorNotFound, NotMasterError, ExecutionTimeout, or
OperationFailure.
:Parameters:
- `response`: byte string as returned from the database
- `cursor_id` (optional): cursor_id we sent to get this response -
used for raising an informative exception when we get cursor id not
valid at server response
- `codec_options` (optional): an instance of
:class:`~bson.codec_options.CodecOptions`
"""
response_flag = struct.unpack("<i", response[:4])[0]
if response_flag & 1:
# Shouldn't get this response if we aren't doing a getMore
assert cursor_id is not None
# Fake a getMore command response. OP_GET_MORE provides no document.
msg = "Cursor not found, cursor id: %d" % (cursor_id,)
errobj = {"ok": 0, "errmsg": msg, "code": 43}
raise CursorNotFound(msg, 43, errobj)
elif response_flag & 2:
error_object = bson.BSON(response[20:]).decode()
# Fake the ok field if it doesn't exist.
error_object.setdefault("ok", 0)
if error_object["$err"].startswith("not master"):
raise NotMasterError(error_object["$err"], error_object)
elif error_object.get("code") == 50:
raise ExecutionTimeout(error_object.get("$err"),
error_object.get("code"),
error_object)
raise OperationFailure("database error: %s" %
error_object.get("$err"),
error_object.get("code"),
error_object)
result = {"cursor_id": struct.unpack("<q", response[4:12])[0],
"starting_from": struct.unpack("<i", response[12:16])[0],
"number_returned": struct.unpack("<i", response[16:20])[0],
"data": bson.decode_all(response[20:], codec_options)}
assert len(result["data"]) == result["number_returned"]
return result
