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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,217 @@ | ||
| # Copyright 2017 Oregon Health and Science University | ||
| # | ||
| # Copyright (C) 2015-2021 Regents of the University of California | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
|
|
||
|
|
||
| import ftplib | ||
| import logging | ||
| import netrc | ||
| import os | ||
| from contextlib import closing | ||
| from typing import Optional, Any, cast, IO | ||
| from urllib.parse import urlparse | ||
| from urllib.request import urlopen | ||
|
|
||
| logger = logging.getLogger(__name__) | ||
|
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|
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||
| class FtpFsAccess: | ||
| """ | ||
| FTP access with upload. | ||
| Taken and modified from https://github.com/ohsu-comp-bio/cwl-tes/blob/03f0096f9fae8acd527687d3460a726e09190c3a/cwl_tes/ftp.py#L37-L251 | ||
| """ | ||
| # TODO: Properly support FTP over SSL | ||
|
|
||
| def __init__( | ||
| self, cache: Optional[dict[Any, ftplib.FTP]] = None | ||
| ): | ||
| """ | ||
| FTP object to handle FTP connections. By default, connect over FTP with TLS. | ||
| :param cache: cache of generated FTP objects | ||
| """ | ||
| self.cache = cache or {} | ||
| self.netrc = None | ||
| try: | ||
| if "HOME" in os.environ: | ||
| if os.path.exists(os.path.join(os.environ["HOME"], ".netrc")): | ||
| self.netrc = netrc.netrc(os.path.join(os.environ["HOME"], ".netrc")) | ||
| elif os.path.exists(os.path.join(os.curdir, ".netrc")): | ||
| self.netrc = netrc.netrc(os.path.join(os.curdir, ".netrc")) | ||
| except netrc.NetrcParseError as err: | ||
| logger.debug(err) | ||
|
|
||
| def exists(self, fn: str) -> bool: | ||
| """ | ||
| Check if a file/directory exists over an FTP server | ||
| :param fn: FTP url | ||
| :return: True or false depending on whether the object exists on the server | ||
| """ | ||
| return self.isfile(fn) or self.isdir(fn) | ||
|
|
||
| def isfile(self, fn: str) -> bool: | ||
| """ | ||
| Check if the FTP url points to a file | ||
| :param fn: FTP url | ||
| :return: True if url is file, else false | ||
| """ | ||
| ftp = self._connect(fn) | ||
| if ftp: | ||
| try: | ||
| if not self.size(fn) is None: | ||
| return True | ||
| else: | ||
| return False | ||
| except ftplib.all_errors: | ||
| return False | ||
| return False | ||
|
|
||
| def isdir(self, fn: str) -> bool: | ||
| """ | ||
| Check if the FTP url points to a directory | ||
| :param fn: FTP url | ||
| :return: True if url is directory, else false | ||
| """ | ||
| ftp = self._connect(fn) | ||
| if ftp: | ||
| try: | ||
| cwd = ftp.pwd() | ||
| ftp.cwd(urlparse(fn).path) | ||
| ftp.cwd(cwd) | ||
| return True | ||
| except ftplib.all_errors: | ||
| return False | ||
| return False | ||
|
|
||
| def open(self, fn: str, mode: str) -> IO[bytes]: | ||
| """ | ||
| Open an FTP url. | ||
| Only supports reading, no write support. | ||
| :param fn: FTP url | ||
| :param mode: Mode to open FTP url in | ||
| :return: | ||
| """ | ||
| if "r" in mode: | ||
| host, port, user, passwd, path = self._parse_url(fn) | ||
| handle = urlopen("ftp://{}:{}@{}:{}/{}".format(user, passwd, host, port, path)) | ||
| return cast(IO[bytes], closing(handle)) | ||
| # TODO: support write mode | ||
| raise Exception("Write mode FTP not implemented") | ||
|
|
||
| def _parse_url( | ||
| self, url: str | ||
| ) -> tuple[str, int, Optional[str], Optional[str], str]: | ||
| """ | ||
| Parse an FTP url into hostname, username, password, and path | ||
| :param url: | ||
| :return: hostname, username, password, path | ||
| """ | ||
| parse = urlparse(url) | ||
| user = parse.username | ||
| passwd = parse.password | ||
| host = parse.hostname | ||
| port = parse.port | ||
| path = parse.path | ||
| if host is None: | ||
| # The URL we connect to must have a host | ||
| raise RuntimeError(f"FTP URL does not contain a host: {url}") | ||
| # default port is 21 | ||
| if port is None: | ||
| port = 21 | ||
| if parse.scheme == "ftp": | ||
| if not user and self.netrc: | ||
| if host is not None: | ||
| creds = self.netrc.authenticators(host) | ||
| if creds: | ||
| user, _, passwd = creds | ||
| if not user: | ||
| if host is not None: | ||
| user, passwd = self._recall_credentials(host) | ||
| if passwd is None: | ||
| passwd = "anonymous@" | ||
| if user is None: | ||
| user = "anonymous" | ||
| return host, port, user, passwd, path | ||
|
|
||
| def _connect(self, url: str) -> Optional[ftplib.FTP]: | ||
| """ | ||
| Connect to an FTP server. Handles authentication. | ||
| :param url: FTP url | ||
| :return: FTP object | ||
| """ | ||
| parse = urlparse(url) | ||
| if parse.scheme == "ftp": | ||
| host, port, user, passwd, _ = self._parse_url(url) | ||
| if host is None: | ||
| # there has to be a host | ||
| return None | ||
| if (host, user, passwd) in self.cache: | ||
| if self.cache[(host, user, passwd)].pwd(): | ||
| return self.cache[(host, user, passwd)] | ||
| ftp = ftplib.FTP_TLS() | ||
| # Note: the FTP lib logger handles logging itself and doesn't go through our logging implementation | ||
| ftp.set_debuglevel(1 if logger.isEnabledFor(logging.DEBUG) else 0) | ||
| ftp.connect(host, port) | ||
| env_user = os.getenv("TOIL_FTP_USER") | ||
| env_passwd = os.getenv("TOIL_FTP_PASSWORD") | ||
| if env_user: | ||
| user = env_user | ||
| if env_passwd: | ||
| passwd = env_passwd | ||
| ftp.login(user or "", passwd or "", secure=False) | ||
| self.cache[(host, user, passwd)] = ftp | ||
| return ftp | ||
| return None | ||
|
|
||
| def _recall_credentials( | ||
| self, desired_host: str | ||
| ) -> tuple[Optional[str], Optional[str]]: | ||
| """ | ||
| Grab the cached credentials | ||
| :param desired_host: FTP hostname | ||
| :return: username, password | ||
| """ | ||
| for host, user, passwd in self.cache: | ||
| if desired_host == host: | ||
| return user, passwd | ||
| return None, None | ||
|
|
||
| def size(self, fn: str) -> Optional[int]: | ||
| """ | ||
| Get the size of an FTP object | ||
| :param fn: FTP url | ||
| :return: Size of object | ||
| """ | ||
| ftp = self._connect(fn) | ||
| if ftp: | ||
| host, port, user, passwd, path = self._parse_url(fn) | ||
| try: | ||
| return ftp.size(path) | ||
| except ftplib.all_errors as e: | ||
| if str(e) == "550 SIZE not allowed in ASCII mode": | ||
| # some servers don't allow grabbing size in ascii mode | ||
| # https://stackoverflow.com/questions/22090001/get-folder-size-using-ftplib/22093848#22093848 | ||
| ftp.voidcmd("TYPE I") | ||
| return ftp.size(path) | ||
| handle = urlopen("ftp://{}:{}@{}:{}/{}".format(user, passwd, host, port, path)) | ||
| info = handle.info() | ||
| handle.close() | ||
| if "Content-length" in info: | ||
| return int(info["Content-length"]) | ||
| return None | ||
|
|
||
| return None |