medspacy
medspacy.load(enable) seems to ignore "medspacy_quickumls" in the component list
Please check notebook notebook 11a. Cell 4 attempts to enable a list of components including "medspacy_quickumls". Cell 5 displays the components actually loaded. "medspacy_quickumls" is not among them. If one does a manual medspacy.add_pipe("medspacy_quickumls") afterward, it loads fine, so I think there is a flaw in the enable logic.
@RonWilkinson Are you running this notebook on Windows? If so, QuickUMLS (and therefore medspacy_quickumls) are not installed by default. Did you run through these steps to install QuickUMLS manually following the medspacy install?
https://github.com/medspacy/medspacy/blob/master/windows_and_quickumls.md
I’m running on Linux. In any case, in my note I point out that I a manual add_pipe works when Load(activate) does not. Add_pipe would not work if medspacy_quickumls were not installed.
--Ron
From: Kelly Peterson @.> Sent: Thursday, November 3, 2022 12:54 PM To: medspacy/medspacy @.> Cc: Wilkinson, Ronald @.>; Mention @.> Subject: Re: [medspacy/medspacy] medspacy.load(enable) seems to ignore "medspacy_quickumls" in the component list (Issue #167) [EXTERNAL]
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You are right. Thank you for re-iterating that behavior. We will look into this.
We are about to release a new medspacy version (1.1). After that is released and stable, either @turbosheep or myself can fix this so that "medspacy_quickumls" will be uncommented from this block in util.py:
ALL_PIPE_NAMES = {
"medspacy_tokenizer",
"medspacy_preprocessor",
"medspacy_pyrush",
"medspacy_target_matcher",
# "medspacy_quickumls", # quickumls still not included by default due to install issues
"medspacy_context",
"medspacy_sectionizer",
"medspacy_postprocessor",
"medspacy_doc_consumer",
}
In other words, we will fix this, but I think we want to make sure we have at least a stable week of new usage before we flip the switch.
@turbosheep This should be possible to fix now with 1.1.2. Could you add a test for this to make sure it works with medspacy.load().
hi @burgersmoke I'm encountering the same issue. I'm running on linux and have medspacy 1.1.2, medspacy-quickumls 3.0 installed. Manual adding by nlp.add_pipe("medspacy_quickumls") works.
concurrent medspacy and quickumls installation results in this error message when adding pipe: ValueError: [E002] Can't find factory for 'medspacy_quickumls' for language English (en). the error is reproducible when running notebook 11b, python 3.11, in venv with medspacy and quickumls installed.
managed to initialize UMLS resources by running this with python 3.8 without installing quickumls: python -m quickumls.install <umls_installation_path> <destination_path>
@ivcvy Are you unblocked at the moment then? Sorry we don't have a lot of additional time to address issues since medspacy is something we support on the side of other work priorities.
I did want to make sure that you are running again since I would not have expected that the error you report:
Can't find factory for 'medspacy_quickumls' for language English
to have been solved by generating UMLS resources. The error above to me looks like python module for quickumls not being imported before any calls to
nlp.add_pipe("medspacy_quickumls")
(whether as a part of madspacy.load() or a manual call)
@burgersmoke Thank you for your support. My intention was to use full UMLS resource using medspacy_quickumls and it works at the moment. I did not intend to install quickumls and use it as standalone, but I thought I have to install quickumls before generating UMLS resource (following the guide).
