scTM could not be imported

[hanyuefuqu8]

Hello, I installed scTM using pip, but I could not import it, it seems caused by unavailable of this website: http://www.immunesinglecell.org/api/vishuo/getToolkitUrl
here's part of my stderr:
File /usr/local/python3/python3.8.10/lib/python3.8/site-packages/discotoolkit/GlobalVariable.py:20
17 timeout = 600
19 # Define package-level variable
---> 20 response = requests.get("http://www.immunesinglecell.org/api/vishuo/getToolkitUrl")
22 if response.status_code == 200:
23 prefix_disco_url = json.loads(response.text)["url"]

File /usr/local/python3/python3.8.10/lib/python3.8/site-packages/requests/api.py:73, in get(url, params, **kwargs)
62 def get(url, params=None, **kwargs):
63 r"""Sends a GET request.
64
65 :param url: URL for the new :class:Request object.
(...)
70 :rtype: requests.Response
71 """
---> 73 return request("get", url, params=params, **kwargs)

File /usr/local/python3/python3.8.10/lib/python3.8/site-packages/requests/api.py:59, in request(method, url, **kwargs)
55 # By using the 'with' statement we are sure the session is closed, thus we
56 # avoid leaving sockets open which can trigger a ResourceWarning in some
57 # cases, and look like a memory leak in others.
58 with sessions.Session() as session:
---> 59 return session.request(method=method, url=url, **kwargs)

File /usr/local/python3/python3.8.10/lib/python3.8/site-packages/requests/sessions.py:589, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
584 send_kwargs = {
585 "timeout": timeout,
586 "allow_redirects": allow_redirects,
587 }
588 send_kwargs.update(settings)
--> 589 resp = self.send(prep, **send_kwargs)
591 return resp

File /usr/local/python3/python3.8.10/lib/python3.8/site-packages/requests/sessions.py:703, in Session.send(self, request, **kwargs)
700 start = preferred_clock()
702 # Send the request
--> 703 r = adapter.send(request, **kwargs)
705 # Total elapsed time of the request (approximately)
706 elapsed = preferred_clock() - start

File /usr/local/python3/python3.8.10/lib/python3.8/site-packages/requests/adapters.py:519, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
515 if isinstance(e.reason, _SSLError):
516 # This branch is for urllib3 v1.22 and later.
517 raise SSLError(e, request=request)
--> 519 raise ConnectionError(e, request=request)
521 except ClosedPoolError as e:
522 raise ConnectionError(e, request=request)

ConnectionError: HTTPConnectionPool(host='www.immunesinglecell.org', port=80): Max retries exceeded with url: /api/vishuo/getToolkitUrl (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7faff19912b0>: Failed to establish a new connection: [Errno 110] Connection timed out'))

I'm not sure if this is the reason, could you pls help me?

[Chengwei94]

@hanyuefuqu8

do you still face the problem? I thik there was a issue with immunesinglecell 2 days ago that causes this problem

[zyd1235]

你好，这是我的报错，他是说在import scTM的时候必须联网吗，有可以不联网导入的方法吗

TimeoutError Traceback (most recent call last)
File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:174, in HTTPConnection._new_conn(self)
173 try:
--> 174 conn = connection.create_connection(
175 (self._dns_host, self.port), self.timeout, **extra_kw
176 )
178 except SocketTimeout:

File /opt/software/python/lib/python3.8/site-packages/urllib3/util/connection.py:95, in create_connection(address, timeout, source_address, socket_options)
94 if err is not None:
---> 95 raise err
97 raise socket.error("getaddrinfo returns an empty list")

File /opt/software/python/lib/python3.8/site-packages/urllib3/util/connection.py:85, in create_connection(address, timeout, source_address, socket_options)
84 sock.bind(source_address)
---> 85 sock.connect(sa)
86 return sock

TimeoutError: [Errno 110] Connection timed out

During handling of the above exception, another exception occurred:

NewConnectionError Traceback (most recent call last)
File /opt/software/python/lib/python3.8/site-packages/urllib3/connectionpool.py:703, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
702 # Make the request on the httplib connection object.
--> 703 httplib_response = self._make_request(
704 conn,
705 method,
706 url,
707 timeout=timeout_obj,
708 body=body,
709 headers=headers,
710 chunked=chunked,
711 )
713 # If we're going to release the connection in finally:, then
714 # the response doesn't need to know about the connection. Otherwise
715 # it will also try to release it and we'll have a double-release
716 # mess.

File /opt/software/python/lib/python3.8/site-packages/urllib3/connectionpool.py:398, in HTTPConnectionPool._make_request(self, conn, method, url, timeout, chunked, **httplib_request_kw)
397 else:
--> 398 conn.request(method, url, **httplib_request_kw)
400 # We are swallowing BrokenPipeError (errno.EPIPE) since the server is
401 # legitimately able to close the connection after sending a valid response.
402 # With this behaviour, the received response is still readable.

File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:239, in HTTPConnection.request(self, method, url, body, headers)
238 headers["User-Agent"] = _get_default_user_agent()
--> 239 super(HTTPConnection, self).request(method, url, body=body, headers=headers)

File /opt/software/python/lib/python3.8/http/client.py:1256, in HTTPConnection.request(self, method, url, body, headers, encode_chunked)
1255 """Send a complete request to the server."""
-> 1256 self._send_request(method, url, body, headers, encode_chunked)

File /opt/software/python/lib/python3.8/http/client.py:1302, in HTTPConnection._send_request(self, method, url, body, headers, encode_chunked)
1301 body = _encode(body, 'body')
-> 1302 self.endheaders(body, encode_chunked=encode_chunked)

File /opt/software/python/lib/python3.8/http/client.py:1251, in HTTPConnection.endheaders(self, message_body, encode_chunked)
1250 raise CannotSendHeader()
-> 1251 self._send_output(message_body, encode_chunked=encode_chunked)

File /opt/software/python/lib/python3.8/http/client.py:1011, in HTTPConnection._send_output(self, message_body, encode_chunked)
1010 del self._buffer[:]
-> 1011 self.send(msg)
1013 if message_body is not None:
1014
1015 # create a consistent interface to message_body

File /opt/software/python/lib/python3.8/http/client.py:951, in HTTPConnection.send(self, data)
950 if self.auto_open:
--> 951 self.connect()
952 else:

File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:205, in HTTPConnection.connect(self)
204 def connect(self):
--> 205 conn = self._new_conn()
206 self._prepare_conn(conn)

File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:186, in HTTPConnection._new_conn(self)
185 except SocketError as e:
--> 186 raise NewConnectionError(
187 self, "Failed to establish a new connection: %s" % e
188 )
190 return conn

NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fbbad13fc40>: Failed to establish a new connection: [Errno 110] Connection timed out

During handling of the above exception, another exception occurred:

MaxRetryError Traceback (most recent call last)
File /opt/software/python/lib/python3.8/site-packages/requests/adapters.py:489, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
488 if not chunked:
--> 489 resp = conn.urlopen(
490 method=request.method,
491 url=url,
492 body=request.body,
493 headers=request.headers,
494 redirect=False,
495 assert_same_host=False,
496 preload_content=False,
497 decode_content=False,
498 retries=self.max_retries,
499 timeout=timeout,
500 )
502 # Send the request.
503 else:

File /opt/software/python/lib/python3.8/site-packages/urllib3/connectionpool.py:787, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
785 e = ProtocolError("Connection aborted.", e)
--> 787 retries = retries.increment(
788 method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
789 )
790 retries.sleep()

File /opt/software/python/lib/python3.8/site-packages/urllib3/util/retry.py:592, in Retry.increment(self, method, url, response, error, _pool, _stacktrace)
591 if new_retry.is_exhausted():
--> 592 raise MaxRetryError(_pool, url, error or ResponseError(cause))
594 log.debug("Incremented Retry for (url='%s'): %r", url, new_retry)

MaxRetryError: HTTPConnectionPool(host='www.immunesinglecell.org', port=80): Max retries exceeded with url: /api/vishuo/getToolkitUrl (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fbbad13fc40>: Failed to establish a new connection: [Errno 110] Connection timed out'))

During handling of the above exception, another exception occurred:

ConnectionError Traceback (most recent call last)
Cell In [12], line 2
1 # 尝试再次导入包
----> 2 import sctm

File /opt/software/python/lib/python3.8/site-packages/sctm/init.py:7
4 email = "chengwei8@gmail.com"
5 version = "0.1.0"
----> 7 from . import analysis, metrics, pl, pp, seed, stamp, utils
9 all = ["pl", "pp", "analysis", "stamp", "utils", "metrics", "seed"]

File /opt/software/python/lib/python3.8/site-packages/sctm/analysis.py:1
----> 1 import discotoolkit as dt
2 import gseapy as gp
3 from joblib import Parallel, delayed

File /opt/software/python/lib/python3.8/site-packages/discotoolkit/init.py:1
----> 1 from .GetMetadata import *
2 from .DiscoClass import *
3 from .DownloadDiscoData import *

File /opt/software/python/lib/python3.8/site-packages/discotoolkit/GetMetadata.py:13
10 from typing import Union
12 # import variable and class from other script
---> 13 from .GlobalVariable import logging, prefix_disco_url
14 from .DiscoClass import FilterData, Filter
16 def get_json(url : str, info_msg: str, error_msg: str, prefix : bool = True):

File /opt/software/python/lib/python3.8/site-packages/discotoolkit/GlobalVariable.py:20
17 timeout = 600
19 # Define package-level variable
---> 20 response = requests.get("http://www.immunesinglecell.org/api/vishuo/getToolkitUrl")
22 if response.status_code == 200:
23 prefix_disco_url = json.loads(response.text)["url"]

File /opt/software/python/lib/python3.8/site-packages/requests/api.py:73, in get(url, params, **kwargs)
62 def get(url, params=None, **kwargs):
63 r"""Sends a GET request.
64
65 :param url: URL for the new :class:Request object.
(...)
70 :rtype: requests.Response
71 """
---> 73 return request("get", url, params=params, **kwargs)

File /opt/software/python/lib/python3.8/site-packages/requests/api.py:59, in request(method, url, **kwargs)
55 # By using the 'with' statement we are sure the session is closed, thus we
56 # avoid leaving sockets open which can trigger a ResourceWarning in some
57 # cases, and look like a memory leak in others.
58 with sessions.Session() as session:
---> 59 return session.request(method=method, url=url, **kwargs)

File /opt/software/python/lib/python3.8/site-packages/requests/sessions.py:587, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
582 send_kwargs = {
583 "timeout": timeout,
584 "allow_redirects": allow_redirects,
585 }
586 send_kwargs.update(settings)
--> 587 resp = self.send(prep, **send_kwargs)
589 return resp

File /opt/software/python/lib/python3.8/site-packages/requests/sessions.py:701, in Session.send(self, request, **kwargs)
698 start = preferred_clock()
700 # Send the request
--> 701 r = adapter.send(request, **kwargs)
703 # Total elapsed time of the request (approximately)
704 elapsed = preferred_clock() - start

File /opt/software/python/lib/python3.8/site-packages/requests/adapters.py:565, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
561 if isinstance(e.reason, _SSLError):
562 # This branch is for urllib3 v1.22 and later.
563 raise SSLError(e, request=request)
--> 565 raise ConnectionError(e, request=request)
567 except ClosedPoolError as e:
568 raise ConnectionError(e, request=request)

ConnectionError: HTTPConnectionPool(host='www.immunesinglecell.org', port=80): Max retries exceeded with url: /api/vishuo/getToolkitUrl (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fbbad13fc40>: Failed to establish a new connection: [Errno 110] Connection timed out'))

[hanyuefuqu8]

你好，这是我的报错，他是说在import scTM的时候必须联网吗，有可以不联网导入的方法吗

TimeoutError Traceback (most recent call last) File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:174, in HTTPConnection._new_conn(self) 173 try: --> 174 conn = connection.create_connection( 175 (self._dns_host, self.port), self.timeout, **extra_kw 176 ) 178 except SocketTimeout:

File /opt/software/python/lib/python3.8/site-packages/urllib3/util/connection.py:95, in create_connection(address, timeout, source_address, socket_options) 94 if err is not None: ---> 95 raise err 97 raise socket.error("getaddrinfo returns an empty list")

File /opt/software/python/lib/python3.8/site-packages/urllib3/util/connection.py:85, in create_connection(address, timeout, source_address, socket_options) 84 sock.bind(source_address) ---> 85 sock.connect(sa) 86 return sock

TimeoutError: [Errno 110] Connection timed out

During handling of the above exception, another exception occurred:

NewConnectionError Traceback (most recent call last) File /opt/software/python/lib/python3.8/site-packages/urllib3/connectionpool.py:703, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw) 702 # Make the request on the httplib connection object. --> 703 httplib_response = self._make_request( 704 conn, 705 method, 706 url, 707 timeout=timeout_obj, 708 body=body, 709 headers=headers, 710 chunked=chunked, 711 ) 713 # If we're going to release the connection in finally:, then 714 # the response doesn't need to know about the connection. Otherwise 715 # it will also try to release it and we'll have a double-release 716 # mess.

File /opt/software/python/lib/python3.8/site-packages/urllib3/connectionpool.py:398, in HTTPConnectionPool._make_request(self, conn, method, url, timeout, chunked, **httplib_request_kw) 397 else: --> 398 conn.request(method, url, **httplib_request_kw) 400 # We are swallowing BrokenPipeError (errno.EPIPE) since the server is 401 # legitimately able to close the connection after sending a valid response. 402 # With this behaviour, the received response is still readable.

File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:239, in HTTPConnection.request(self, method, url, body, headers) 238 headers["User-Agent"] = _get_default_user_agent() --> 239 super(HTTPConnection, self).request(method, url, body=body, headers=headers)

File /opt/software/python/lib/python3.8/http/client.py:1256, in HTTPConnection.request(self, method, url, body, headers, encode_chunked) 1255 """Send a complete request to the server.""" -> 1256 self._send_request(method, url, body, headers, encode_chunked)

File /opt/software/python/lib/python3.8/http/client.py:1302, in HTTPConnection._send_request(self, method, url, body, headers, encode_chunked) 1301 body = _encode(body, 'body') -> 1302 self.endheaders(body, encode_chunked=encode_chunked)

File /opt/software/python/lib/python3.8/http/client.py:1251, in HTTPConnection.endheaders(self, message_body, encode_chunked) 1250 raise CannotSendHeader() -> 1251 self._send_output(message_body, encode_chunked=encode_chunked)

File /opt/software/python/lib/python3.8/http/client.py:1011, in HTTPConnection._send_output(self, message_body, encode_chunked) 1010 del self._buffer[:] -> 1011 self.send(msg) 1013 if message_body is not None: 1014 1015 # create a consistent interface to message_body

File /opt/software/python/lib/python3.8/http/client.py:951, in HTTPConnection.send(self, data) 950 if self.auto_open: --> 951 self.connect() 952 else:

File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:205, in HTTPConnection.connect(self) 204 def connect(self): --> 205 conn = self._new_conn() 206 self._prepare_conn(conn)

File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:186, in HTTPConnection._new_conn(self) 185 except SocketError as e: --> 186 raise NewConnectionError( 187 self, "Failed to establish a new connection: %s" % e 188 ) 190 return conn

NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fbbad13fc40>: Failed to establish a new connection: [Errno 110] Connection timed out

During handling of the above exception, another exception occurred:

MaxRetryError Traceback (most recent call last) File /opt/software/python/lib/python3.8/site-packages/requests/adapters.py:489, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies) 488 if not chunked: --> 489 resp = conn.urlopen( 490 method=request.method, 491 url=url, 492 body=request.body, 493 headers=request.headers, 494 redirect=False, 495 assert_same_host=False, 496 preload_content=False, 497 decode_content=False, 498 retries=self.max_retries, 499 timeout=timeout, 500 ) 502 # Send the request. 503 else:

File /opt/software/python/lib/python3.8/site-packages/urllib3/connectionpool.py:787, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw) 785 e = ProtocolError("Connection aborted.", e) --> 787 retries = retries.increment( 788 method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2] 789 ) 790 retries.sleep()

File /opt/software/python/lib/python3.8/site-packages/urllib3/util/retry.py:592, in Retry.increment(self, method, url, response, error, _pool, _stacktrace) 591 if new_retry.is_exhausted(): --> 592 raise MaxRetryError(_pool, url, error or ResponseError(cause)) 594 log.debug("Incremented Retry for (url='%s'): %r", url, new_retry)

MaxRetryError: HTTPConnectionPool(host='www.immunesinglecell.org', port=80): Max retries exceeded with url: /api/vishuo/getToolkitUrl (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fbbad13fc40>: Failed to establish a new connection: [Errno 110] Connection timed out'))

During handling of the above exception, another exception occurred:

ConnectionError Traceback (most recent call last) Cell In [12], line 2 1 # 尝试再次导入包 ----> 2 import sctm

File /opt/software/python/lib/python3.8/site-packages/sctm/init.py:7 4 email = "chengwei8@gmail.com" 5 version = "0.1.0" ----> 7 from . import analysis, metrics, pl, pp, seed, stamp, utils 9 all = ["pl", "pp", "analysis", "stamp", "utils", "metrics", "seed"]

File /opt/software/python/lib/python3.8/site-packages/sctm/analysis.py:1 ----> 1 import discotoolkit as dt 2 import gseapy as gp 3 from joblib import Parallel, delayed

File /opt/software/python/lib/python3.8/site-packages/discotoolkit/init.py:1 ----> 1 from .GetMetadata import * 2 from .DiscoClass import * 3 from .DownloadDiscoData import *

File /opt/software/python/lib/python3.8/site-packages/discotoolkit/GetMetadata.py:13 10 from typing import Union 12 # import variable and class from other script ---> 13 from .GlobalVariable import logging, prefix_disco_url 14 from .DiscoClass import FilterData, Filter 16 def get_json(url : str, info_msg: str, error_msg: str, prefix : bool = True):

File /opt/software/python/lib/python3.8/site-packages/discotoolkit/GlobalVariable.py:20 17 timeout = 600 19 # Define package-level variable ---> 20 response = requests.get("http://www.immunesinglecell.org/api/vishuo/getToolkitUrl") 22 if response.status_code == 200: 23 prefix_disco_url = json.loads(response.text)["url"]

File /opt/software/python/lib/python3.8/site-packages/requests/api.py:73, in get(url, params, **kwargs) 62 def get(url, params=None, **kwargs): 63 r"""Sends a GET request. 64 65 :param url: URL for the new :class:Request object. (...) 70 :rtype: requests.Response 71 """ ---> 73 return request("get", url, params=params, **kwargs)

File /opt/software/python/lib/python3.8/site-packages/requests/api.py:59, in request(method, url, **kwargs) 55 # By using the 'with' statement we are sure the session is closed, thus we 56 # avoid leaving sockets open which can trigger a ResourceWarning in some 57 # cases, and look like a memory leak in others. 58 with sessions.Session() as session: ---> 59 return session.request(method=method, url=url, **kwargs)

File /opt/software/python/lib/python3.8/site-packages/requests/sessions.py:587, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json) 582 send_kwargs = { 583 "timeout": timeout, 584 "allow_redirects": allow_redirects, 585 } 586 send_kwargs.update(settings) --> 587 resp = self.send(prep, **send_kwargs) 589 return resp

File /opt/software/python/lib/python3.8/site-packages/requests/sessions.py:701, in Session.send(self, request, **kwargs) 698 start = preferred_clock() 700 # Send the request --> 701 r = adapter.send(request, **kwargs) 703 # Total elapsed time of the request (approximately) 704 elapsed = preferred_clock() - start

File /opt/software/python/lib/python3.8/site-packages/requests/adapters.py:565, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies) 561 if isinstance(e.reason, _SSLError): 562 # This branch is for urllib3 v1.22 and later. 563 raise SSLError(e, request=request) --> 565 raise ConnectionError(e, request=request) 567 except ClosedPoolError as e: 568 raise ConnectionError(e, request=request)

ConnectionError: HTTPConnectionPool(host='www.immunesinglecell.org', port=80): Max retries exceeded with url: /api/vishuo/getToolkitUrl (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fbbad13fc40>: Failed to establish a new connection: [Errno 110] Connection timed out'))

Hello, I installed it successfully later. I think it is necessary to connect to the Internet

[zyd1235]

感谢您的解答，但是我的命令是import不是install也必须联网吗

…

---- 回复的原邮件 ---- | 发件人 | ***@***.***> | | 日期 | 2024年12月31日 10:10 | | 收件人 | ***@***.***> | | 抄送至 | ***@***.***>***@***.***> | | 主题 | Re: [JinmiaoChenLab/scTM] scTM could not be imported (Issue #4) | 你好，这是我的报错，他是说在import scTM的时候必须联网吗，有可以不联网导入的方法吗 TimeoutError Traceback (most recent call last) File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:174, in HTTPConnection._new_conn(self) 173 try: --> 174 conn = connection.create_connection( 175 (self._dns_host, self.port), self.timeout, **extra_kw 176 ) 178 except SocketTimeout: File /opt/software/python/lib/python3.8/site-packages/urllib3/util/connection.py:95, in create_connection(address, timeout, source_address, socket_options) 94 if err is not None: ---> 95 raise err 97 raise socket.error("getaddrinfo returns an empty list") File /opt/software/python/lib/python3.8/site-packages/urllib3/util/connection.py:85, in create_connection(address, timeout, source_address, socket_options) 84 sock.bind(source_address) ---> 85 sock.connect(sa) 86 return sock TimeoutError: [Errno 110] Connection timed out During handling of the above exception, another exception occurred: NewConnectionError Traceback (most recent call last) File /opt/software/python/lib/python3.8/site-packages/urllib3/connectionpool.py:703, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw) 702 # Make the request on the httplib connection object. --> 703 httplib_response = self._make_request( 704 conn, 705 method, 706 url, 707 timeout=timeout_obj, 708 body=body, 709 headers=headers, 710 chunked=chunked, 711 ) 713 # If we're going to release the connection in finally:, then 714 # the response doesn't need to know about the connection. Otherwise 715 # it will also try to release it and we'll have a double-release 716 # mess. File /opt/software/python/lib/python3.8/site-packages/urllib3/connectionpool.py:398, in HTTPConnectionPool._make_request(self, conn, method, url, timeout, chunked, **httplib_request_kw) 397 else: --> 398 conn.request(method, url, **httplib_request_kw) 400 # We are swallowing BrokenPipeError (errno.EPIPE) since the server is 401 # legitimately able to close the connection after sending a valid response. 402 # With this behaviour, the received response is still readable. File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:239, in HTTPConnection.request(self, method, url, body, headers) 238 headers["User-Agent"] = _get_default_user_agent() --> 239 super(HTTPConnection, self).request(method, url, body=body, headers=headers) File /opt/software/python/lib/python3.8/http/client.py:1256, in HTTPConnection.request(self, method, url, body, headers, encode_chunked) 1255 """Send a complete request to the server.""" -> 1256 self._send_request(method, url, body, headers, encode_chunked) File /opt/software/python/lib/python3.8/http/client.py:1302, in HTTPConnection._send_request(self, method, url, body, headers, encode_chunked) 1301 body = _encode(body, 'body') -> 1302 self.endheaders(body, encode_chunked=encode_chunked) File /opt/software/python/lib/python3.8/http/client.py:1251, in HTTPConnection.endheaders(self, message_body, encode_chunked) 1250 raise CannotSendHeader() -> 1251 self._send_output(message_body, encode_chunked=encode_chunked) File /opt/software/python/lib/python3.8/http/client.py:1011, in HTTPConnection._send_output(self, message_body, encode_chunked) 1010 del self._buffer[:] -> 1011 self.send(msg) 1013 if message_body is not None: 1014 1015 # create a consistent interface to message_body File /opt/software/python/lib/python3.8/http/client.py:951, in HTTPConnection.send(self, data) 950 if self.auto_open: --> 951 self.connect() 952 else: File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:205, in HTTPConnection.connect(self) 204 def connect(self): --> 205 conn = self._new_conn() 206 self._prepare_conn(conn) File /opt/software/python/lib/python3.8/site-packages/urllib3/connection.py:186, in HTTPConnection._new_conn(self) 185 except SocketError as e: --> 186 raise NewConnectionError( 187 self, "Failed to establish a new connection: %s" % e 188 ) 190 return conn NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fbbad13fc40>: Failed to establish a new connection: [Errno 110] Connection timed out During handling of the above exception, another exception occurred: MaxRetryError Traceback (most recent call last) File /opt/software/python/lib/python3.8/site-packages/requests/adapters.py:489, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies) 488 if not chunked: --> 489 resp = conn.urlopen( 490 method=request.method, 491 url=url, 492 body=request.body, 493 headers=request.headers, 494 redirect=False, 495 assert_same_host=False, 496 preload_content=False, 497 decode_content=False, 498 retries=self.max_retries, 499 timeout=timeout, 500 ) 502 # Send the request. 503 else: File /opt/software/python/lib/python3.8/site-packages/urllib3/connectionpool.py:787, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw) 785 e = ProtocolError("Connection aborted.", e) --> 787 retries = retries.increment( 788 method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2] 789 ) 790 retries.sleep() File /opt/software/python/lib/python3.8/site-packages/urllib3/util/retry.py:592, in Retry.increment(self, method, url, response, error, _pool, _stacktrace) 591 if new_retry.is_exhausted(): --> 592 raise MaxRetryError(_pool, url, error or ResponseError(cause)) 594 log.debug("Incremented Retry for (url='%s'): %r", url, new_retry) MaxRetryError: HTTPConnectionPool(host='www.immunesinglecell.org', port=80): Max retries exceeded with url: /api/vishuo/getToolkitUrl (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fbbad13fc40>: Failed to establish a new connection: [Errno 110] Connection timed out')) During handling of the above exception, another exception occurred: ConnectionError Traceback (most recent call last) Cell In [12], line 2 1 # 尝试再次导入包 ----> 2 import sctm File /opt/software/python/lib/python3.8/site-packages/sctm/init.py:7 4 email = ***@***.***" 5 version = "0.1.0" ----> 7 from . import analysis, metrics, pl, pp, seed, stamp, utils 9 all = ["pl", "pp", "analysis", "stamp", "utils", "metrics", "seed"] File /opt/software/python/lib/python3.8/site-packages/sctm/analysis.py:1 ----> 1 import discotoolkit as dt 2 import gseapy as gp 3 from joblib import Parallel, delayed File /opt/software/python/lib/python3.8/site-packages/discotoolkit/init.py:1 ----> 1 from .GetMetadata import * 2 from .DiscoClass import * 3 from .DownloadDiscoData import * File /opt/software/python/lib/python3.8/site-packages/discotoolkit/GetMetadata.py:13 10 from typing import Union 12 # import variable and class from other script ---> 13 from .GlobalVariable import logging, prefix_disco_url 14 from .DiscoClass import FilterData, Filter 16 def get_json(url : str, info_msg: str, error_msg: str, prefix : bool = True): File /opt/software/python/lib/python3.8/site-packages/discotoolkit/GlobalVariable.py:20 17 timeout = 600 19 # Define package-level variable ---> 20 response = requests.get("http://www.immunesinglecell.org/api/vishuo/getToolkitUrl") 22 if response.status_code == 200: 23 prefix_disco_url = json.loads(response.text)["url"] File /opt/software/python/lib/python3.8/site-packages/requests/api.py:73, in get(url, params, **kwargs) 62 def get(url, params=None, **kwargs): 63 r"""Sends a GET request. 64 65 :param url: URL for the new :class:Request object. (...) 70 :rtype: requests.Response 71 """ ---> 73 return request("get", url, params=params, **kwargs) File /opt/software/python/lib/python3.8/site-packages/requests/api.py:59, in request(method, url, **kwargs) 55 # By using the 'with' statement we are sure the session is closed, thus we 56 # avoid leaving sockets open which can trigger a ResourceWarning in some 57 # cases, and look like a memory leak in others. 58 with sessions.Session() as session: ---> 59 return session.request(method=method, url=url, **kwargs) File /opt/software/python/lib/python3.8/site-packages/requests/sessions.py:587, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json) 582 send_kwargs = { 583 "timeout": timeout, 584 "allow_redirects": allow_redirects, 585 } 586 send_kwargs.update(settings) --> 587 resp = self.send(prep, **send_kwargs) 589 return resp File /opt/software/python/lib/python3.8/site-packages/requests/sessions.py:701, in Session.send(self, request, **kwargs) 698 start = preferred_clock() 700 # Send the request --> 701 r = adapter.send(request, **kwargs) 703 # Total elapsed time of the request (approximately) 704 elapsed = preferred_clock() - start File /opt/software/python/lib/python3.8/site-packages/requests/adapters.py:565, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies) 561 if isinstance(e.reason, _SSLError): 562 # This branch is for urllib3 v1.22 and later. 563 raise SSLError(e, request=request) --> 565 raise ConnectionError(e, request=request) 567 except ClosedPoolError as e: 568 raise ConnectionError(e, request=request) ConnectionError: HTTPConnectionPool(host='www.immunesinglecell.org', port=80): Max retries exceeded with url: /api/vishuo/getToolkitUrl (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fbbad13fc40>: Failed to establish a new connection: [Errno 110] Connection timed out')) Hello, I installed it successfully later. I think it is necessary to connect to the Internet — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>