class FsMongo(FsBase):
def __init__(self, logger_name='fs', lock=False):
super().__init__(logger_name, lock)
self.path = None
self.client = None
self.fs = None
def __update_local_fs(self, from_path=None):
dir_cursor = self.fs.find({"metadata.type": "dir"},
no_cursor_timeout=True)
for directory in dir_cursor:
if from_path and not directory.filename.startswith(from_path):
continue
os.makedirs(self.path + directory.filename, exist_ok=True)
file_cursor = self.fs.find({"metadata.type": {
"$in": ["file", "sym"]
}},
no_cursor_timeout=True)
for writing_file in file_cursor:
if from_path and not writing_file.filename.startswith(from_path):
continue
file_path = self.path + writing_file.filename
if writing_file.metadata["type"] == "sym":
with BytesIO() as b:
self.fs.download_to_stream(writing_file._id, b)
b.seek(0)
link = b.read().decode("utf-8")
try:
os.remove(file_path)
except OSError as e:
if e.errno != errno.ENOENT:
# This is probably permission denied or worse
raise
os.symlink(link, file_path)
else:
with open(file_path, 'wb+') as file_stream:
self.fs.download_to_stream(writing_file._id, file_stream)
if "permissions" in writing_file.metadata:
os.chmod(file_path, writing_file.metadata["permissions"])
def get_params(self):
return {"fs": "mongo", "path": self.path}
def fs_connect(self, config):
try:
if "logger_name" in config:
self.logger = logging.getLogger(config["logger_name"])
if "path" in config:
self.path = config["path"]
else:
raise FsException("Missing parameter \"path\"")
if not self.path.endswith("/"):
self.path += "/"
if not os.path.exists(self.path):
raise FsException(
"Invalid configuration param at '[storage]': path '{}' does not exist"
.format(config["path"]))
elif not os.access(self.path, os.W_OK):
raise FsException(
"Invalid configuration param at '[storage]': path '{}' is not writable"
.format(config["path"]))
if all(key in config.keys() for key in ["uri", "collection"]):
self.client = MongoClient(config["uri"])
self.fs = GridFSBucket(self.client[config["collection"]])
elif all(key in config.keys()
for key in ["host", "port", "collection"]):
self.client = MongoClient(config["host"], config["port"])
self.fs = GridFSBucket(self.client[config["collection"]])
else:
if "collection" not in config.keys():
raise FsException("Missing parameter \"collection\"")
else:
raise FsException(
"Missing parameters: \"uri\" or \"host\" + \"port\"")
except FsException:
raise
except Exception as e: # TODO refine
raise FsException(str(e))
def fs_disconnect(self):
pass # TODO
def mkdir(self, folder):
"""
Creates a folder or parent object location
:param folder:
:return: None or raises an exception
"""
try:
self.fs.upload_from_stream(folder,
BytesIO(),
metadata={"type": "dir"})
except errors.FileExists: # make it idempotent
pass
except Exception as e:
raise FsException(str(e),
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
def dir_rename(self, src, dst):
"""
Rename one directory name. If dst exist, it replaces (deletes) existing directory
:param src: source directory
:param dst: destination directory
:return: None or raises and exception
"""
try:
dst_cursor = self.fs.find(
{"filename": {
"$regex": "^{}(/|$)".format(dst)
}},
no_cursor_timeout=True)
for dst_file in dst_cursor:
self.fs.delete(dst_file._id)
src_cursor = self.fs.find(
{"filename": {
"$regex": "^{}(/|$)".format(src)
}},
no_cursor_timeout=True)
for src_file in src_cursor:
self.fs.rename(src_file._id,
src_file.filename.replace(src, dst, 1))
except Exception as e:
raise FsException(str(e),
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
def file_exists(self, storage, mode=None):
"""
Indicates if "storage" file exist
:param storage: can be a str or a str list
:param mode: can be 'file' exist as a regular file; 'dir' exists as a directory or; 'None' just exists
:return: True, False
"""
f = storage if isinstance(storage, str) else "/".join(storage)
cursor = self.fs.find({"filename": f})
for requested_file in cursor:
exception_file = next(cursor, None)
if exception_file:
raise FsException("Multiple files found",
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
if requested_file.metadata["type"] == mode:
return True
if requested_file.metadata["type"] == "sym" and mode == "file":
return True
return False
def file_size(self, storage):
"""
return file size
:param storage: can be a str or a str list
:return: file size
"""
f = storage if isinstance(storage, str) else "/".join(storage)
cursor = self.fs.find({"filename": f})
for requested_file in cursor:
exception_file = next(cursor, None)
if exception_file:
raise FsException("Multiple files found",
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
return requested_file.length
def file_extract(self, tar_object, path):
"""
extract a tar file
:param tar_object: object of type tar
:param path: can be a str or a str list, or a tar object where to extract the tar_object
:return: None
"""
f = path if isinstance(path, str) else "/".join(path)
for member in tar_object.getmembers():
if member.isfile():
stream = tar_object.extractfile(member)
elif member.issym():
stream = BytesIO(member.linkname.encode("utf-8"))
else:
stream = BytesIO()
if member.isfile():
file_type = "file"
elif member.issym():
file_type = "sym"
else:
file_type = "dir"
metadata = {"type": file_type, "permissions": member.mode}
self.fs.upload_from_stream(f + "/" + member.name,
stream,
metadata=metadata)
stream.close()
def file_open(self, storage, mode):
"""
Open a file
:param storage: can be a str or list of str
:param mode: file mode
:return: file object
"""
try:
f = storage if isinstance(storage, str) else "/".join(storage)
if "b" in mode:
return GridByteStream(f, self.fs, mode)
else:
return GridStringStream(f, self.fs, mode)
except errors.NoFile:
raise FsException("File {} does not exist".format(f),
http_code=HTTPStatus.NOT_FOUND)
except IOError:
raise FsException("File {} cannot be opened".format(f),
http_code=HTTPStatus.BAD_REQUEST)
def dir_ls(self, storage):
"""
return folder content
:param storage: can be a str or list of str
:return: folder content
"""
try:
f = storage if isinstance(storage, str) else "/".join(storage)
files = []
dir_cursor = self.fs.find({"filename": f})
for requested_dir in dir_cursor:
exception_dir = next(dir_cursor, None)
if exception_dir:
raise FsException(
"Multiple directories found",
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
if requested_dir.metadata["type"] != "dir":
raise FsException("File {} does not exist".format(f),
http_code=HTTPStatus.NOT_FOUND)
files_cursor = self.fs.find(
{"filename": {
"$regex": "^{}/([^/])*".format(f)
}})
for children_file in files_cursor:
files += [children_file.filename.replace(f + '/', '', 1)]
return files
except IOError:
raise FsException("File {} cannot be opened".format(f),
http_code=HTTPStatus.BAD_REQUEST)
def file_delete(self, storage, ignore_non_exist=False):
"""
Delete storage content recursively
:param storage: can be a str or list of str
:param ignore_non_exist: not raise exception if storage does not exist
:return: None
"""
try:
f = storage if isinstance(storage, str) else "/".join(storage)
file_cursor = self.fs.find({"filename": f})
found = False
for requested_file in file_cursor:
found = True
exception_file = next(file_cursor, None)
if exception_file:
raise FsException(
"Multiple files found",
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
if requested_file.metadata["type"] == "dir":
dir_cursor = self.fs.find(
{"filename": {
"$regex": "^{}".format(f)
}})
for tmp in dir_cursor:
self.fs.delete(tmp._id)
else:
self.fs.delete(requested_file._id)
if not found and not ignore_non_exist:
raise FsException("File {} does not exist".format(storage),
http_code=HTTPStatus.NOT_FOUND)
except IOError as e:
raise FsException("File {} cannot be deleted: {}".format(f, e),
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
def sync(self, from_path=None):
"""
Sync from FSMongo to local storage
:param from_path: if supplied, only copy content from this path, not all
:return: None
"""
self.__update_local_fs(from_path=from_path)
class FsMongo(FsBase):
def __init__(self, logger_name='fs', lock=False):
super().__init__(logger_name, lock)
self.path = None
self.client = None
self.fs = None
def __update_local_fs(self, from_path=None):
dir_cursor = self.fs.find({"metadata.type": "dir"},
no_cursor_timeout=True)
for directory in dir_cursor:
if from_path and not directory.filename.startswith(from_path):
continue
os.makedirs(self.path + directory.filename, exist_ok=True)
file_cursor = self.fs.find({"metadata.type": {
"$in": ["file", "sym"]
}},
no_cursor_timeout=True)
for writing_file in file_cursor:
if from_path and not writing_file.filename.startswith(from_path):
continue
file_path = self.path + writing_file.filename
if writing_file.metadata["type"] == "sym":
with BytesIO() as b:
self.fs.download_to_stream(writing_file._id, b)
b.seek(0)
link = b.read().decode("utf-8")
try:
os.remove(file_path)
except OSError as e:
if e.errno != errno.ENOENT:
# This is probably permission denied or worse
raise
os.symlink(link, file_path)
else:
with open(file_path, 'wb+') as file_stream:
self.fs.download_to_stream(writing_file._id, file_stream)
if "permissions" in writing_file.metadata:
os.chmod(file_path, writing_file.metadata["permissions"])
def get_params(self):
return {"fs": "mongo", "path": self.path}
def fs_connect(self, config):
try:
if "logger_name" in config:
self.logger = logging.getLogger(config["logger_name"])
if "path" in config:
self.path = config["path"]
else:
raise FsException("Missing parameter \"path\"")
if not self.path.endswith("/"):
self.path += "/"
if not os.path.exists(self.path):
raise FsException(
"Invalid configuration param at '[storage]': path '{}' does not exist"
.format(config["path"]))
elif not os.access(self.path, os.W_OK):
raise FsException(
"Invalid configuration param at '[storage]': path '{}' is not writable"
.format(config["path"]))
if all(key in config.keys() for key in ["uri", "collection"]):
self.client = MongoClient(config["uri"])
self.fs = GridFSBucket(self.client[config["collection"]])
elif all(key in config.keys()
for key in ["host", "port", "collection"]):
self.client = MongoClient(config["host"], config["port"])
self.fs = GridFSBucket(self.client[config["collection"]])
else:
if "collection" not in config.keys():
raise FsException("Missing parameter \"collection\"")
else:
raise FsException(
"Missing parameters: \"uri\" or \"host\" + \"port\"")
except FsException:
raise
except Exception as e: # TODO refine
raise FsException(str(e))
def fs_disconnect(self):
pass # TODO
def mkdir(self, folder):
"""
Creates a folder or parent object location
:param folder:
:return: None or raises an exception
"""
try:
self.fs.upload_from_stream(folder,
BytesIO(),
metadata={"type": "dir"})
except errors.FileExists: # make it idempotent
pass
except Exception as e:
raise FsException(str(e),
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
def dir_rename(self, src, dst):
"""
Rename one directory name. If dst exist, it replaces (deletes) existing directory
:param src: source directory
:param dst: destination directory
:return: None or raises and exception
"""
try:
dst_cursor = self.fs.find(
{"filename": {
"$regex": "^{}(/|$)".format(dst)
}},
no_cursor_timeout=True)
for dst_file in dst_cursor:
self.fs.delete(dst_file._id)
src_cursor = self.fs.find(
{"filename": {
"$regex": "^{}(/|$)".format(src)
}},
no_cursor_timeout=True)
for src_file in src_cursor:
self.fs.rename(src_file._id,
src_file.filename.replace(src, dst, 1))
except Exception as e:
raise FsException(str(e),
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
def file_exists(self, storage, mode=None):
"""
Indicates if "storage" file exist
:param storage: can be a str or a str list
:param mode: can be 'file' exist as a regular file; 'dir' exists as a directory or; 'None' just exists
:return: True, False
"""
f = storage if isinstance(storage, str) else "/".join(storage)
cursor = self.fs.find({"filename": f})
for requested_file in cursor:
exception_file = next(cursor, None)
if exception_file:
raise FsException("Multiple files found",
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
# if no special mode is required just check it does exists
if not mode:
return True
if requested_file.metadata["type"] == mode:
return True
if requested_file.metadata["type"] == "sym" and mode == "file":
return True
return False
def file_size(self, storage):
"""
return file size
:param storage: can be a str or a str list
:return: file size
"""
f = storage if isinstance(storage, str) else "/".join(storage)
cursor = self.fs.find({"filename": f})
for requested_file in cursor:
exception_file = next(cursor, None)
if exception_file:
raise FsException("Multiple files found",
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
return requested_file.length
def file_extract(self, tar_object, path):
"""
extract a tar file
:param tar_object: object of type tar
:param path: can be a str or a str list, or a tar object where to extract the tar_object
:return: None
"""
f = path if isinstance(path, str) else "/".join(path)
for member in tar_object.getmembers():
if member.isfile():
stream = tar_object.extractfile(member)
elif member.issym():
stream = BytesIO(member.linkname.encode("utf-8"))
else:
stream = BytesIO()
if member.isfile():
file_type = "file"
elif member.issym():
file_type = "sym"
else:
file_type = "dir"
metadata = {"type": file_type, "permissions": member.mode}
self.fs.upload_from_stream(f + "/" + member.name,
stream,
metadata=metadata)
stream.close()
def file_open(self, storage, mode):
"""
Open a file
:param storage: can be a str or list of str
:param mode: file mode
:return: file object
"""
try:
f = storage if isinstance(storage, str) else "/".join(storage)
if "b" in mode:
return GridByteStream(f, self.fs, mode)
else:
return GridStringStream(f, self.fs, mode)
except errors.NoFile:
raise FsException("File {} does not exist".format(f),
http_code=HTTPStatus.NOT_FOUND)
except IOError:
raise FsException("File {} cannot be opened".format(f),
http_code=HTTPStatus.BAD_REQUEST)
def dir_ls(self, storage):
"""
return folder content
:param storage: can be a str or list of str
:return: folder content
"""
try:
f = storage if isinstance(storage, str) else "/".join(storage)
files = []
dir_cursor = self.fs.find({"filename": f})
for requested_dir in dir_cursor:
exception_dir = next(dir_cursor, None)
if exception_dir:
raise FsException(
"Multiple directories found",
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
if requested_dir.metadata["type"] != "dir":
raise FsException("File {} does not exist".format(f),
http_code=HTTPStatus.NOT_FOUND)
files_cursor = self.fs.find(
{"filename": {
"$regex": "^{}/([^/])*".format(f)
}})
for children_file in files_cursor:
files += [children_file.filename.replace(f + '/', '', 1)]
return files
except IOError:
raise FsException("File {} cannot be opened".format(f),
http_code=HTTPStatus.BAD_REQUEST)
def file_delete(self, storage, ignore_non_exist=False):
"""
Delete storage content recursively
:param storage: can be a str or list of str
:param ignore_non_exist: not raise exception if storage does not exist
:return: None
"""
try:
f = storage if isinstance(storage, str) else "/".join(storage)
file_cursor = self.fs.find({"filename": f})
found = False
for requested_file in file_cursor:
found = True
exception_file = next(file_cursor, None)
if exception_file:
raise FsException(
"Multiple files found",
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
if requested_file.metadata["type"] == "dir":
dir_cursor = self.fs.find(
{"filename": {
"$regex": "^{}".format(f)
}})
for tmp in dir_cursor:
self.fs.delete(tmp._id)
else:
self.fs.delete(requested_file._id)
if not found and not ignore_non_exist:
raise FsException("File {} does not exist".format(storage),
http_code=HTTPStatus.NOT_FOUND)
except IOError as e:
raise FsException("File {} cannot be deleted: {}".format(f, e),
http_code=HTTPStatus.INTERNAL_SERVER_ERROR)
def sync(self, from_path=None):
"""
Sync from FSMongo to local storage
:param from_path: if supplied, only copy content from this path, not all
:return: None
"""
if from_path:
if os.path.isabs(from_path):
from_path = os.path.relpath(from_path, self.path)
self.__update_local_fs(from_path=from_path)
def _update_mongo_fs(self, from_path):
os_path = self.path + from_path
# Obtain list of files and dirs in filesystem
members = []
for root, dirs, files in os.walk(os_path):
for folder in dirs:
member = {
"filename": os.path.join(root, folder),
"type": "dir"
}
members.append(member)
for file in files:
filename = os.path.join(root, file)
if os.path.islink(filename):
file_type = "sym"
else:
file_type = "file"
member = {
"filename": os.path.join(root, file),
"type": file_type
}
members.append(member)
# Obtain files in mongo dict
remote_files = self._get_mongo_files(from_path)
# Upload members if they do not exists or have been modified
# We will do this for performance (avoid updating unmodified files) and to avoid
# updating a file with an older one in case there are two sources for synchronization
# in high availability scenarios
for member in members:
# obtain permission
mask = int(oct(os.stat(member["filename"]).st_mode)[-3:], 8)
# convert to relative path
rel_filename = os.path.relpath(member["filename"], self.path)
last_modified_date = datetime.datetime.fromtimestamp(
os.path.getmtime(member["filename"]))
remote_file = remote_files.get(rel_filename)
upload_date = remote_file[
0].uploadDate if remote_file else datetime.datetime.min
# remove processed files from dict
remote_files.pop(rel_filename, None)
if last_modified_date >= upload_date:
stream = None
fh = None
try:
file_type = member["type"]
if file_type == "dir":
stream = BytesIO()
elif file_type == "sym":
stream = BytesIO(
os.readlink(member["filename"]).encode("utf-8"))
else:
fh = open(member["filename"], "rb")
stream = BytesIO(fh.read())
metadata = {"type": file_type, "permissions": mask}
self.fs.upload_from_stream(rel_filename,
stream,
metadata=metadata)
# delete old files
if remote_file:
for file in remote_file:
self.fs.delete(file._id)
finally:
if fh:
fh.close()
if stream:
stream.close()
# delete files that are not any more in local fs
for remote_file in remote_files.values():
for file in remote_file:
self.fs.delete(file._id)
def _get_mongo_files(self, from_path=None):
file_dict = {}
file_cursor = self.fs.find(no_cursor_timeout=True,
sort=[('uploadDate', -1)])
for file in file_cursor:
if from_path and not file.filename.startswith(from_path):
continue
if file.filename in file_dict:
file_dict[file.filename].append(file)
else:
file_dict[file.filename] = [file]
return file_dict
def reverse_sync(self, from_path: str):
"""
Sync from local storage to FSMongo
:param from_path: base directory to upload content to mongo fs
:return: None
"""
if os.path.isabs(from_path):
from_path = os.path.relpath(from_path, self.path)
self._update_mongo_fs(from_path=from_path)
