problem to open tool

[ago-pietra]

The MyoFInDer is installed successfully showing the version is 1.0.10, however when I try to initiate the tool by using the command of python -m myofinder, it tells:

2024-10-15 09:41:28,618 MyoFInDer Launching MyoFInDer
2024-10-15 09:41:28,618 MyoFInDer.MainWindow Creating the splash window
2024-10-15 09:41:28,760 MyoFInDer.MainWindow Centering the splash window
2024-10-15 09:41:29,050 MyoFInDer.MainWindow Displaying the splash window
Downloading data from https://deepcell-data.s3-us-west-1.amazonaws.com/saved-models/MultiplexSegmentation-9.tar.gz
2024-10-15 09:41:37,953 MyoFInDer MyoFInDer encountered an error while running !
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 1346, in do_open
    h.request(req.get_method(), req.selector, req.data, headers,
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 1285, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 1331, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 1280, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 1040, in _send_output
    self.send(msg)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 980, in send
    self.connect()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 1454, in connect
    self.sock = self._context.wrap_socket(self.sock,
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py", line 501, in wrap_socket
    return self.sslsocket_class._create(
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py", line 1041, in _create
    self.do_handshake()
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py", line 1310, in do_handshake
    self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1129)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/keras/utils/data_utils.py", line 277, in get_file
    urlretrieve(origin, fpath, dl_progress)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/keras/utils/data_utils.py", line 82, in urlretrieve
    response = urlopen(url, data)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 214, in urlopen
    return opener.open(url, data, timeout)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 517, in open
    response = self._open(req, data)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 534, in _open
    result = self._call_chain(self.handle_open, protocol, protocol +
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 494, in _call_chain
    result = func(*args)
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 1389, in https_open
    return self.do_open(http.client.HTTPSConnection, req,
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 1349, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1129)>

During handling of the above exception, another exception occurred:

How i can fix it? Thanks lot

[WeisLeDocto]

Hi!

Based on the traceback you provided, I assume you're running Python 3.9 on macOS. The installation of MyoFInDer itself seems functional, the problem is rather at the Python level. The SSL certificates are not installed, or cannot be found by Python.

I haven't experienced this error myself, but I was able to find some guidance on Stack Overflow:

• https://stackoverflow.com/questions/50236117/scraping-ssl-certificate-verify-failed-error-for-http-en-wikipedia-org
• https://stackoverflow.com/questions/27835619/urllib-and-ssl-certificate-verify-failed-error
• https://stackoverflow.com/questions/44649449/brew-installation-of-python-3-6-1-ssl-certificate-verify-failed-certificate/44649450#44649450

Hopefully you can use the workaround provided in the first link, the one in the second link also seems reasonable, and the third one might be outdated as it's already 7 years old but still worth trying if the two first fail.