Lakshidaa
commented
1 month ago Hi @kingljy0818,
Regarding the error you faced while performing download_public_data, we have now retired the downloading of public .hdf5 model files. However, the .onnx model files will still be downloaded. You can find the changes in our latest merge: https://github.com/MolecularAI/aizynthfinder/commit/c18cde13bc1b08bd327ee4d37021c514612021c8. This should resolve your error.
As per the PolicyException you encountered, can you please share more details on this? Specifically, the config.yml file that you used when you encountered this error.
kingljy0818
Hello,
After upgrading AiZynthFinder to version 4.3, I encountered the following error while attempting to run download_public_data my_folder:
(aizynth-env) [root@localhost AiZynthFinder]# download_public_data my_folder Traceback (most recent call last): File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/connection.py", line 198, in _new_conn sock = connection.create_connection( File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/util/connection.py", line 85, in create_connection raise err File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/util/connection.py", line 73, in create_connection sock.connect(sa) ConnectionRefusedError: [Errno 111] Connection refused
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 793, in urlopen response = self._make_request( File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 491, in _make_request raise new_e File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 467, in _make_request self._validate_conn(conn) File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 1099, in _validate_conn conn.connect() File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/connection.py", line 616, in connect self.sock = sock = self._new_conn() File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/connection.py", line 213, in _new_conn raise NewConnectionError( urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f6e51df13f0>: Failed to establish a new connection: [Errno 111] Connection refused
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/requests/adapters.py", line 589, in send resp = conn.urlopen( File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 847, in urlopen retries = retries.increment( File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/urllib3/util/retry.py", line 515, in increment raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='zenodo.org', port=443): Max retries exceeded with url: /record/7341155/files/uspto_keras_model.hdf5 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6e51df13f0>: Failed to establish a new connection: [Errno 111] Connection refused'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/Anaconda3/envs/aizynth-env/bin/download_public_data", line 8, in
sys.exit(main())
File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/aizynthfinder/tools/download_public_data.py", line 89, in main
_download_file(filespec["url"], os.path.join(path, filespec["filename"]))
File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/aizynthfinder/tools/download_public_data.py", line 64, in _download_file
with requests.get(url, stream=True) as response:
File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, kwargs)
File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, kwargs)
File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, send_kwargs)
File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, kwargs)
File "/home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/requests/adapters.py", line 622, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='zenodo.org', port=443): Max retries exceeded with url: /record/7341155/files/uspto_keras_model.hdf5 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f6e51df13f0>: Failed to establish a new connection: [Errno 111] Connection refused'))
I also tried using the previously downloaded 'my_folder', but when running the following code in the notebook:
from aizynthfinder.interfaces import AiZynthApp app = AiZynthApp("config.yml") it showed the following error:"
PolicyException Traceback (most recent call last) Cell In[1], line 2 1 from aizynthfinder.interfaces import AiZynthApp ----> 2 app = AiZynthApp("config.yml")
File /home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/aizynthfinder/interfaces/aizynthapp.py:58, in AiZynthApp.init(self, configfile, setup) 56 def init(self, configfile: str, setup: bool = True) -> None: 57 setup_logger(logging.INFO) ---> 58 self.finder = AiZynthFinder(configfile=configfile) 59 self._input: StrDict = dict() 60 self._output: StrDict = dict()
File /home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/aizynthfinder/aizynthfinder.py:71, in AiZynthFinder.init(self, configfile, configdict) 68 self._logger = logger() 70 if configfile: ---> 71 self.config = Configuration.from_file(configfile) 72 elif configdict: 73 self.config = Configuration.from_dict(configdict)
File /home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/aizynthfinder/context/config.py:141, in Configuration.from_file(cls, filename) 139 txt = txt.replace(item, os.environ[item[2:-1]]) 140 _config = yaml.load(txt, Loader=yaml.SafeLoader) --> 141 return Configuration.from_dict(_config)
File /home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/aizynthfinder/context/config.py:111, in Configuration.from_dict(cls, source) 108 config_obj._update_from_config(dict(source)) 110 config_obj.expansion_policy.load_from_config(expansion_config) --> 111 config_obj.filter_policy.load_from_config(filter_config) 112 config_obj.stock.load_from_config(**stock_config) 113 config_obj.scorers.create_default_scorers()
File /home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/aizynthfinder/context/policy/policies.py:223, in FilterPolicy.load_from_config(self, config) 221 if "type" in kwargs: 222 del kwargs["type"] --> 223 obj = cls(key, self._config, kwargs) 224 self.load(obj)
File /home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/aizynthfinder/context/policy/filter_strategies.py:112, in QuickKerasFilter.init(self, key, config, kwargs) 111 def init(self, key: str, config: Configuration, kwargs: Any) -> None: --> 112 super().init(key, config, **kwargs) 113 source = kwargs["model"] 114 # self.settings = self._config.filter_settings
File /home/Anaconda3/envs/aizynth-env/lib/python3.10/site-packages/aizynthfinder/context/policy/filter_strategies.py:47, in FilterStrategy.init(self, key, config, kwargs) 45 def init(self, key: str, config: Configuration, kwargs: Any) -> None: 46 if any(name not in kwargs for name in self._required_kwargs): ---> 47 raise PolicyException( 48 f"A {self.class.name} class needs to be initiated " 49 f"with keyword arguments: {', '.join(self._required_kwargs)}" 50 ) 51 self._config = config 52 self._logger = logger()
PolicyException: A QuickKerasFilter class needs to be initiated with keyword arguments: model
How can I resolve this issue? I really need your help. Thank you!
Best regards,
Jiyuan