pkpdai / pkner Goto Github PK

Hi, thank you for making your code available here. The project is very interesting and I would like to try running the models on my own data (text from pharmacokinetic literature). I got an error while loading the spacy model following the instructions in the README. I have a conda environment loaded with Python 3.8.12 and installed all dependencies as per the README (including scispacy) -

>>> nlp = spacy.load("en_pk_ner")
Traceback (most recent call last):
File "", line 1, in
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/spacy/init.py", line 50, in load
return util.load_model(
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/spacy/util.py", line 324, in load_model
return load_model_from_package(name, **kwargs)
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/spacy/util.py", line 357, in load_model_from_package
return cls.load(vocab=vocab, disable=disable, exclude=exclude, config=config)
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/en_pk_ner/init.py", line 10, in load
return load_model_from_init_py(file, **overrides)
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/spacy/util.py", line 517, in load_model_from_init_py
return load_model_from_path(
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/spacy/util.py", line 392, in load_model_from_path
nlp = load_model_from_config(config, vocab=vocab, disable=disable, exclude=exclude)
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/spacy/util.py", line 429, in load_model_from_config
nlp = lang_cls.from_config(
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/spacy/language.py", line 1672, in from_config
nlp.add_pipe(
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/spacy/language.py", line 774, in add_pipe
pipe_component = self.create_pipe(
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/spacy/language.py", line 660, in create_pipe
resolved = registry.resolve(cfg, validate=validate)
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/thinc/config.py", line 746, in resolve
resolved, _ = cls._make(
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/thinc/config.py", line 795, in _make
filled, _, resolved = cls._fill(
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/thinc/config.py", line 850, in _fill
filled[key], validation[v_key], final[key] = cls._fill(
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/thinc/config.py", line 849, in _fill
promise_schema = cls.make_promise_schema(value, resolve=resolve)
File "/home/sanya/.conda/envs/ner/lib/python3.8/site-packages/thinc/config.py", line 1057, in make_promise_schema
return create_model("ArgModel", **sig_args)
File "pydantic/main.py", line 990, in pydantic.main.create_model
File "pydantic/main.py", line 299, in pydantic.main.ModelMetaclass.new
File "pydantic/fields.py", line 411, in pydantic.fields.ModelField.infer
File "pydantic/fields.py", line 342, in pydantic.fields.ModelField.init
File "pydantic/fields.py", line 451, in pydantic.fields.ModelField.prepare
File "pydantic/fields.py", line 550, in pydantic.fields.ModelField._type_analysis
File "/home/sanya/.conda/envs/ner/lib/python3.8/typing.py", line 774, in subclasscheck
return issubclass(cls, self.origin)
TypeError: issubclass() arg 1 must be a class

I found this related issue and followed instructions to fix - https://stackoverflow.com/questions/77037891/typeerror-issubclass-arg-1-must-be-a-class and was able to get it to work after adding the following 2 lines in the requirements. Just wanted to add here in case someone else has the same issue. Thanks again!

typing-inspect==0.8.0
typing_extensions==4.5.0