unable to download models

[mxiang1]

Hi, I have been seeing the same timeout error message when trying to download models in both command line and python versions:

import celltypist from celltypist import models models.download_models(model = 'Immune_All_Low.pkl') 📜 Retrieving model list from server https://celltypist.cog.sanger.ac.uk/models/models.json Traceback (most recent call last): File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 386, in _make_request self._validate_conn(conn) File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 1042, in _validate_conn conn.connect() File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/connection.py", line 419, in connect self.sock = ssl_wrapsocket( File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/util/ssl.py", line 449, in ssl_wrap_socket ssl_sock = _ssl_wrap_socketimpl( File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/util/ssl.py", line 493, in _ssl_wrap_socket_impl return ssl_context.wrap_socket(sock, server_hostname=server_hostname) File "/share/software/user/open/python/3.9.0/lib/python3.9/ssl.py", line 500, in wrap_socket return self.sslsocket_class._create( File "/share/software/user/open/python/3.9.0/lib/python3.9/ssl.py", line 1040, in _create self.do_handshake() File "/share/software/user/open/python/3.9.0/lib/python3.9/ssl.py", line 1309, in do_handshake self._sslobj.do_handshake() socket.timeout: _ssl.c:1105: The handshake operation timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/users/mxiang1/.local/lib/python3.9/site-packages/requests/adapters.py", line 489, in send resp = conn.urlopen( File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 787, in urlopen retries = retries.increment( File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/util/retry.py", line 550, in increment raise six.reraise(type(error), error, _stacktrace) File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/packages/six.py", line 770, in reraise raise value File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 703, in urlopen httplib_response = self._make_request( File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 389, in _make_request self._raise_timeout(err=e, url=url, timeout_value=conn.timeout) File "/home/users/mxiang1/.local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 340, in _raise_timeout raise ReadTimeoutError( urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='celltypist.cog.sanger.ac.uk', port=443): Read timed out. (read timeout=30)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/users/mxiang1/.local/lib/python3.9/site-packages/celltypist/models.py", line 38, in _requests_get r = requests.get(url, timeout = timeout) File "/home/users/mxiang1/.local/lib/python3.9/site-packages/requests/api.py", line 73, in get return request("get", url, params=params, kwargs) File "/home/users/mxiang1/.local/lib/python3.9/site-packages/requests/api.py", line 59, in request return session.request(method=method, url=url, kwargs) File "/home/users/mxiang1/.local/lib/python3.9/site-packages/requests/sessions.py", line 587, in request resp = self.send(prep, send_kwargs) File "/home/users/mxiang1/.local/lib/python3.9/site-packages/requests/sessions.py", line 701, in send r = adapter.send(request, kwargs) File "/home/users/mxiang1/.local/lib/python3.9/site-packages/requests/adapters.py", line 578, in send raise ReadTimeout(e, request=request) requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='celltypist.cog.sanger.ac.uk', port=443): Read timed out. (read timeout=30)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "", line 1, in File "/home/users/mxiang1/.local/lib/python3.9/site-packages/celltypist/models.py", line 436, in download_models models_json = get_models_index(force_update) File "/home/users/mxiang1/.local/lib/python3.9/site-packages/celltypist/models.py", line 395, in get_models_index download_model_index() File "/home/users/mxiang1/.local/lib/python3.9/site-packages/celltypist/models.py", line 412, in download_model_index response = _requests_get(url) File "/home/users/mxiang1/.local/lib/python3.9/site-packages/celltypist/models.py", line 41, in _requests_get raise Exception( Exception: 🛑 Cannot fetch 'https://celltypist.cog.sanger.ac.uk/models/models.json', the error is: HTTPSConnectionPool(host='celltypist.cog.sanger.ac.uk', port=443): Read timed out. (read timeout=30)

I tried increasing read_timeout but it didn't change anything. Could you look into this? Thanks!

[prete]

Hi @mxiang1, thank you for using CellTypists.

Can you check if you can access the URL from a web broswer in the same network? Paste this in your browser: https://celltypist.cog.sanger.ac.uk/models/models.json does it load properly?

From the same environment you can try to retrieve the model list using wget or curl.

wget -O models.json https://celltypist.cog.sanger.ac.uk/models/models.json

Does that work?

If some of those still don't work, then it may be an issue with the web proxy on your network that's blocking the URL.

[mxiang1]

Hi Prete,

​I tested the wget command and also failed to connect.

$ wget -O models.json https://celltypist.cog.sanger.ac.uk/models/models.json
--2023-11-17 08:59:00--  https://celltypist.cog.sanger.ac.uk/models/models.json
Resolving celltypist.cog.sanger.ac.uk (celltypist.cog.sanger.ac.uk)... 193.62.203.62, 193.62.203.63, 193.62.203.61
Connecting to celltypist.cog.sanger.ac.uk (celltypist.cog.sanger.ac.uk)|193.62.203.62|:443... connected.

Unable to establish SSL connection.

I'm connecting from our institutional HPC and the support team told me there seems to be a restriction put in place on the Sanger side which doesn't accept connections from Stanford systems.

[edg1983]

The same is happening here.

Any attempt to download a model using the python API in our HPC fails due to connection timeout.

However, manual download from the browser in my personal laptop seems to work fine.

[IsaacUtah1379]

I'm having the same problem. The Python API and wget fail due to connection timeout on the HPC I'm using but downloading from my desktop works fine.