EntityLinker import not working

[akki248]

Hi everyone,

I'm unable to import the scispacy EntityLinker using the code:

import spacy
import scispacy

from scispacy.linking import EntityLinker

When I run this piece of code in the Jupyter lab, the cell does not run and probably the kernel dies or restarts. I'm not sure what exactly is happening.

Details which might be useful:

Please also find the packages installed in the environment:

# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: osx-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/osx-64/_py-xgboost-mutex-2.0-cpu_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/blas-1.0-mkl.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/c-ares-1.17.1-h0d85af4_1.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/ca-certificates-2021.5.25-hecd8cb5_1.conda
https://conda.anaconda.org/anaconda/osx-64/fribidi-1.0.10-haf1e3a3_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/intel-openmp-2021.2.0-hecd8cb5_564.conda
https://conda.anaconda.org/anaconda/osx-64/jpeg-9b-he5867d9_2.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/libcxx-11.1.0-habf9029_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/libgfortran-3.0.1-h93005f0_2.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/libiconv-1.16-h1de35cc_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/libsodium-1.0.18-h1de35cc_0.conda
https://conda.anaconda.org/conda-forge/osx-64/llvm-openmp-11.1.0-hda6cdc1_1.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/pandoc-2.12-hecd8cb5_0.conda
https://conda.anaconda.org/anaconda/osx-64/pixman-0.40.0-haf1e3a3_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/xz-5.2.5-h1de35cc_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/yaml-0.2.5-haf1e3a3_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/zlib-1.2.11-h1de35cc_3.conda
https://repo.anaconda.com/pkgs/main/osx-64/expat-2.3.0-h23ab428_2.conda
https://conda.anaconda.org/anaconda/osx-64/graphite2-1.3.14-h38d11af_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/hdf5-1.10.6-hdbbcd12_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/icu-58.2-h0a44026_3.conda
https://conda.anaconda.org/conda-forge/osx-64/libcrc32c-1.1.1-h1c7c35f_2.tar.bz2
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https://conda.anaconda.org/conda-forge/osx-64/libprotobuf-3.16.0-hcf210ce_0.tar.bz2
https://conda.anaconda.org/conda-forge/osx-64/libxgboost-1.4.0-he49afe7_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/lz4-c-1.9.2-h79c402e_3.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/mkl-2021.2.0-hecd8cb5_269.conda
https://repo.anaconda.com/pkgs/main/osx-64/ncurses-6.2-h0a44026_1.conda
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https://repo.anaconda.com/pkgs/main/osx-64/openssl-1.1.1k-h9ed2024_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/pcre-8.44-hb1e8313_0.conda
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https://conda.anaconda.org/anaconda/osx-64/fontconfig-2.13.0-h5d5b041_1.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/gettext-0.21.0-h7535e17_0.conda
https://conda.anaconda.org/anaconda/osx-64/libtiff-4.1.0-hcb84e12_1.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/sqlite-3.35.4-hce871da_0.conda
https://conda.anaconda.org/anaconda/osx-64/glib-2.56.2-hd9629dc_0.tar.bz2
https://conda.anaconda.org/anaconda/osx-64/lcms2-2.11-h92f6f08_0.tar.bz2
https://repo.anaconda.com/pkgs/main/osx-64/python-3.8.8-h88f2d9e_5.conda
https://repo.anaconda.com/pkgs/main/osx-64/qt-5.9.7-h468cd18_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/appnope-0.1.2-py38hecd8cb5_1001.conda
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https://repo.anaconda.com/pkgs/main/noarch/dictdiffer-0.8.0-py_0.conda
https://repo.anaconda.com/pkgs/main/noarch/dill-0.3.3-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/docutils-0.17.1-py38hecd8cb5_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/entrypoints-0.3-py38_0.conda
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https://conda.anaconda.org/conda-forge/noarch/funcy-1.16-pyhd8ed1ab_0.tar.bz2
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https://conda.anaconda.org/conda-forge/noarch/tqdm-4.60.0-pyhd8ed1ab_0.tar.bz2
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https://repo.anaconda.com/pkgs/main/osx-64/glue-core-0.15.6-py38hecd8cb5_0.conda
https://conda.anaconda.org/conda-forge/osx-64/py-xgboost-1.4.0-py38h50d1736_0.tar.bz2
https://repo.anaconda.com/pkgs/main/noarch/pynndescent-0.5.2-pyhd3eb1b0_0.conda
https://repo.anaconda.com/pkgs/main/noarch/glue-vispy-viewers-0.12.2-py_0.conda
https://repo.anaconda.com/pkgs/main/osx-64/opentsne-0.3.11-py38h1de35cc_1.conda
https://repo.anaconda.com/pkgs/main/osx-64/glueviz-1.0.0-0.conda
https://repo.anaconda.com/pkgs/main/osx-64/orange3-3.26.0-py38hb1e8313_0.conda

Please help.
Thanks.

[dakinggg]

Pretty hard to debug without an error message. Can you run that code as a script and see if you get an error message?

[akki248]

Thanks. Here, it is:

[dakinggg]

My guess is that something is not working on 20.0.4, but its a bit hard to know without digging further. The prime candidate is nmslib. Can you see if you are able to install and import nmslib separately from scispacy?

[akki248]

Thanks again. I was able to install the nmslib library and was able to import the EntityLinker. All seems fine now. :)
But, I get a warning when I add the spacy linker pipe to my trained NER model.

[dakinggg]

Great! That warning is not anything to worry about, just a warning from sklearn.