QuickUMLS
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Georgetown-IR-Lab
__init__() got an unexpected keyword argument 'spacy_component'
Describe the bug
When I run the following code:
from quickumls.spacy_component import SpacyQuickUMLS
nlp = spacy.load('en_core_web_sm') quickumls_component = SpacyQuickUMLS(nlp, '/home/silverock/umls/quickUMLS') nlp.add_pipe(quickumls_component)
I got this message:
TypeError Traceback (most recent call last)
~/anaconda3/lib/python3.8/site-packages/quickumls/spacy_component.py in init(self, nlp, quickumls_fp, best_match, ignore_syntax, **kwargs) 23 """ 24 ---> 25 self.quickumls = QuickUMLS(quickumls_fp, 26 # By default, the QuickUMLS objects creates its own internal spacy pipeline but this is not needed 27 # when we're using it as a component in a pipeline
TypeError: init() got an unexpected keyword argument 'spacy_component'
Could you solve this issue?
**My Environment **
- OS: Ubuntu 20.04
- QuickUMLS version 1.4
- UMLS version: 2020AB
- spacy 2.4.5
- Python 3.8.5
I think I'm getting a similar error to this. It tells me there is "no such module" as spacy_component.
@eunsuk-c I got this error too. Apparently pip install quickumls didn't install the latest commit as seen in this repo. At least that's the case for me and I don't know why. When I checked the core.py in my environment against the core.py as seen in the repo, I got these differences below. So, perhaps you might want to check if this is the case in your environment?
Without looking through all of the diff output below, the spacy_component = False argument is missing in the init function of the QuickUMLS Class in core.py that got installed. So I simply replaced the core.py in my environment with the latest version from this repo that has the spacy_component argument.
After updatingcore.py, I was able to instantiate SpacyQuickUMLS(nlp, '<path to quick umls data>'). That being said, this whole pipeline does not work with SpaCy 3.0, but since you're using spaCy 2.4.5, I'm assuming this is not an issue for you.
$ diff -w /Users/<username>/opt/anaconda3/envs/quickUMLS/lib/python3.7/site-packages/quickumls/core.py QuickUMLS/quickumls/core.py
29c29,30
< verbose=False, keep_uppercase=False):
---
> verbose=False, keep_uppercase=False,
> spacy_component = False):
148a150,154
> # if this is not being executed as as spacy component, then it must be standalone
> if spacy_component:
> # In this case, the pipeline is external to this current class
> self.nlp = None
> else:
325d330
< for cui, semtypes, preferred in cuisem_match:
331a337
>
334a341,342
> for cui, semtypes, preferred in cuisem_match:
>
438a447,468
> # pass in parsed spacy doc to get concept matches
> matches = self._match(parsed)
>
> return matches
>
> def _match(self, doc, best_match=True, ignore_syntax=False):
> """Gathers ngram matches given a spaCy document object.
>
> [extended_summary]
>
> Args:
> text (Document): spaCy Document object to be used for extracting ngrams
>
> best_match (bool, optional): Whether to return only the top match or all overlapping candidates. Defaults to True.
> ignore_syntax (bool, optional): Wether to use the heuristcs introduced in the paper (Soldaini and Goharian, 2016). TODO: clarify,. Defaults to False
>
> Returns:
> List: List of all matches in the text
> TODO: Describe format
> """
>
> ngrams = None
440c470
< ngrams = self._make_token_sequences(parsed)
---
> ngrams = self._make_token_sequences(doc)
442c472
< ngrams = self._make_ngrams(parsed)
---
> ngrams = self._make_ngrams(doc)
449c479
< self._print_verbose_status(parsed, matches)
---
> self._print_verbose_status(doc, matches)
(quickUMLS) Suruthais-MacBook-Pro:UMLS noonscape$ diff -b /Users/noonscape/opt/anaconda3/envs/quickUMLS/lib/python3.7/site-packages/quickumls/core.py QuickUMLS/quickumls/core.py
29c29,30
< verbose=False, keep_uppercase=False):
---
> verbose=False, keep_uppercase=False,
> spacy_component = False):
148a150,154
> # if this is not being executed as as spacy component, then it must be standalone
> if spacy_component:
> # In this case, the pipeline is external to this current class
> self.nlp = None
> else:
325d330
< for cui, semtypes, preferred in cuisem_match:
331a337
>
334a341,342
> for cui, semtypes, preferred in cuisem_match:
>
438a447,468
> # pass in parsed spacy doc to get concept matches
> matches = self._match(parsed)
>
> return matches
>
> def _match(self, doc, best_match=True, ignore_syntax=False):
> """Gathers ngram matches given a spaCy document object.
>
> [extended_summary]
>
> Args:
> text (Document): spaCy Document object to be used for extracting ngrams
>
> best_match (bool, optional): Whether to return only the top match or all overlapping candidates. Defaults to True.
> ignore_syntax (bool, optional): Wether to use the heuristcs introduced in the paper (Soldaini and Goharian, 2016). TODO: clarify,. Defaults to False
>
> Returns:
> List: List of all matches in the text
> TODO: Describe format
> """
>
> ngrams = None
440c470
< ngrams = self._make_token_sequences(parsed)
---
> ngrams = self._make_token_sequences(doc)
442c472
< ngrams = self._make_ngrams(parsed)
---
> ngrams = self._make_ngrams(doc)
449c479
< self._print_verbose_status(parsed, matches)
---
> self._print_verbose_status(doc, matches)
My Environment
- OS: Mac OS X Big Sur
- QuickUMLS version 1.4 (I installed this Feb 2021)
- UMLS version: 2019AM
- Spacy 3.0 (Note that there are other issues with SpacCy 3.0 and this library)
- Python 3.7
I think I'm getting a similar error to this. It tells me there is "no such module" as
spacy_component.
@jimhavrilla I had this error as well. For some reasons, when I installed this library with pip install quickumls, the spacy_component.py did not get installed in my environment site packages. Perhaps, that's also what happened with your install?
I had to manually put spacy_component.py where the rest of the module files are for this to work.
My Environment
- OS: Mac OS X Big Sur
- QuickUMLS version 1.4 (I installed this Feb 2021)
- UMLS version: 2019AB
- Spacy 3.0 (Note that there are other issues with SpacCy 3.0 and this library)
- Python 3.7
- anaconda environment
Yes, this seems to be correct. I also got some weird bug during install where if I tried to run pip install again it kept trying to reinstall spaCy 3.0. Possibly related to what you said?
Jim Havrilla
On Fri, Feb 26, 2021, 8:31 AM Noon Pokaratsiri Goldstein < [email protected]> wrote:
I think I'm getting a similar error to this. It tells me there is "no such module" as spacy_component.
@jimhavrilla https://github.com/jimhavrilla I had this error as well. For some reasons, when I installed this library with pip install quickumls, the spacy_component.py did not get installed in my environment site packages. Perhaps, that's also what happened with your install? I had to manually put spacy_component.py where the rest of the module files are for this to work.
My Environment
- OS: Mac OS X Big Sur
- QuickUMLS version 1.4 (I installed this Feb 2021)
- UMLS version: 2019AB
- Spacy 3.0 (Note that there are other issues with SpacCy 3.0 and this library)
- Python 3.7
- anaconda environment
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@DSLituiev As a part of medspacy, we have started our own fork of QuickUMLS. In this fork, we support spacy v3.x and we have addressed this issue with version 2.5 of medspacy_quickumls.
Please note if you decide to consider any of the options below which address this, please note that as a medspacy team, we have elected to no longer support leveldb as a database backend since we've encountered problems and we do not have time or resources to troubleshoot and fix these.
That repo is here: https://github.com/medspacy/QuickUMLS
It's also now pip-installable here: https://pypi.org/project/medspacy-quickumls/
