Add the abbreviation pipe to the spacy pipeline.

nlp.add_pipe("abbreviation_detector")

doc = nlp("Spinal and bulbar muscular atrophy (SBMA) is an \ inherited motor neuron disease caused by the expansion \ of a polyglutamine tract within the androgen receptor (AR). \ SBMA can be caused by this easily.")

print("Abbreviation", "\t", "Definition") for abrv in doc..abbreviations: print(f"{abrv} \t ({abrv.start}, {abrv.end}) {abrv..long_form}")


```log
Traceback (most recent call last):
  File "/home/zhangx/a_project/p_supersimpletransformers_20211128/vega_test_sicspacy_demo.py", line 16, in <module>
    nlp.add_pipe("abbreviation_detector")
  File "/home/zhangx/anaconda3/envs/vega_scispacy/lib/python3.9/site-packages/spacy/language.py", line 801, in add_pipe
    pipe_component = self.create_pipe(
  File "/home/zhangx/anaconda3/envs/vega_scispacy/lib/python3.9/site-packages/spacy/language.py", line 661, in create_pipe
    raise ValueError(err)
ValueError: [E002] Can't find factory for 'abbreviation_detector' for language English (en). This usually happens when spaCy calls `nlp.create_pipe` with a custom component name that's not registered on the current language class. If you're using a Transformer, make sure to install 'spacy-transformers'. If you're using a custom component, make sure you've added the decorator `@Language.component` (for function components) or `@Language.factory` (for class components).

Available factories: attribute_ruler, tok2vec, merge_noun_chunks, merge_entities, merge_subtokens, token_splitter, doc_cleaner, parser, beam_parser, lemmatizer, trainable_lemmatizer, entity_linker, ner, beam_ner, entity_ruler, tagger, morphologizer, senter, sentencizer, textcat, spancat, future_entity_ruler, span_ruler, textcat_multilabel, en.lemmatizer

vegaviazhang commented 1 year ago

the package i install is 1.pip install scispacy 2.pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_core_sci_sm-0.5.1.tar.gz

dakinggg commented 1 year ago

Hi, I just copied all of your commands and code exactly and it worked for me. Could you please try again?

vegaviazhang commented 1 year ago

Hi, I just copied all of your commands and code exactly and it worked for me. Could you please try again?

Okay, I'll try again and write the outcome.

vegaviazhang commented 1 year ago

I'm coming. I run the follow command. 1.conda create --name vega_scispacy_2 python=3.9 -y 2.conda activate vega_scispacy_2 3.pip list 4.pip install scispacy 5.pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_core_sci_sm-0.5.1.tar.gz 6.vim demo_scispacy.py and copy the demo code 7.cat demo_scispacy.py 8.pip list|grep scispacy 9.pip list|grep en_core_sci 10.python -V 11.python demo_scispacy.py 12.I Got Success result, Hey.

13.But I don't know why the previous error, unbelieveable.

The all log are as following.

(base) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ conda create --name vega_scispacy_2 python=3.9 -y
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.9.2
  latest version: 22.11.1

Please update conda by running

    $ conda update -n base -c defaults conda

## Package Plan ##

  environment location: /home/zhangx/anaconda3/envs/vega_scispacy_2

  added / updated specs:
    - python=3.9

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
  ca-certificates    pkgs/main/linux-64::ca-certificates-2022.10.11-h06a4308_0
  certifi            pkgs/main/linux-64::certifi-2022.9.24-py39h06a4308_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
  libffi             pkgs/main/linux-64::libffi-3.4.2-h6a678d5_6
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
  ncurses            pkgs/main/linux-64::ncurses-6.3-h5eee18b_3
  openssl            pkgs/main/linux-64::openssl-1.1.1s-h7f8727e_0
  pip                pkgs/main/linux-64::pip-22.3.1-py39h06a4308_0
  python             pkgs/main/linux-64::python-3.9.15-h7a1cb2a_2
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0
  setuptools         pkgs/main/linux-64::setuptools-65.5.0-py39h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.40.0-h5082296_0
  tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0
  tzdata             pkgs/main/noarch::tzdata-2022g-h04d1e81_0
  wheel              pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.8-h5eee18b_0
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate vega_scispacy_2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ conda activate vega_scispacy_2
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ conda activate vega_scispacy_2
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ pip list
Package    Version
---------- ---------
certifi    2022.9.24
pip        22.3.1
setuptools 65.5.0
wheel      0.37.1
WARNING: The repository located at pypi.douban.com is not a trusted or secure host and is being ignored. If this repository is available via HTTPS we recommend you use HTTPS instead, otherwise you may silence this warning and allow it anyway with '--trusted-host pypi.douban.com'.
WARNING: There was an error checking the latest version of pip.
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ pip install scispacy
Looking in indexes: http://pypi.douban.com/simple
Collecting scispacy
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Installing collected packages: wasabi, cymem, urllib3, typing-extensions, tqdm, threadpoolctl, spacy-loggers, spacy-legacy, smart-open, pysbd, pybind11, psutil, packaging, numpy, murmurhash, MarkupSafe, langcodes, joblib, idna, conllu, click, charset-normalizer, catalogue, typer, srsly, scipy, requests, pydantic, preshed, nmslib, jinja2, blis, scikit-learn, pathy, confection, thinc, spacy, scispacy
Successfully installed MarkupSafe-2.1.1 blis-0.7.9 catalogue-2.0.8 charset-normalizer-2.1.1 click-8.1.3 confection-0.0.3 conllu-4.5.2 cymem-2.0.7 idna-3.4 jinja2-3.1.2 joblib-1.2.0 langcodes-3.3.0 murmurhash-1.0.9 nmslib-2.1.1 numpy-1.23.5 packaging-22.0 pathy-0.10.1 preshed-3.0.8 psutil-5.9.4 pybind11-2.6.1 pydantic-1.10.2 pysbd-0.3.4 requests-2.28.1 scikit-learn-1.2.0 scipy-1.9.3 scispacy-0.5.1 smart-open-6.3.0 spacy-3.4.3 spacy-legacy-3.0.10 spacy-loggers-1.0.4 srsly-2.4.5 thinc-8.1.5 threadpoolctl-3.1.0 tqdm-4.64.1 typer-0.7.0 typing-extensions-4.4.0 urllib3-1.26.13 wasabi-0.10.1
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_core_sci_sm-0.5.1.tar.gz
Looking in indexes: http://pypi.douban.com/simple
Collecting https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_core_sci_sm-0.5.1.tar.gz
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Building wheels for collected packages: en-core-sci-sm
  Building wheel for en-core-sci-sm (setup.py) ... done
  Created wheel for en-core-sci-sm: filename=en_core_sci_sm-0.5.1-py3-none-any.whl size=15870856 sha256=e99e476d22293a04ce498b2a9a3ed2514cdadebb4b9fa5794ebf40b51d05587c
  Stored in directory: /home/zhangx/.cache/pip/wheels/f5/2e/39/9c9d425a1d34c06409420f7c65c5e10a56f7b149a3c37cdfa6
Successfully built en-core-sci-sm
Installing collected packages: en-core-sci-sm
Successfully installed en-core-sci-sm-0.5.1
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ vim demo_scispacy.py
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ cat demo_scispacy.py
import spacy

from scispacy.abbreviation import AbbreviationDetector

nlp = spacy.load("en_core_sci_sm")

# Add the abbreviation pipe to the spacy pipeline.
nlp.add_pipe("abbreviation_detector")

doc = nlp("Spinal and bulbar muscular atrophy (SBMA) is an \
           inherited motor neuron disease caused by the expansion \
           of a polyglutamine tract within the androgen receptor (AR). \
           SBMA can be caused by this easily.")

print("Abbreviation", "\t", "Definition")
for abrv in doc._.abbreviations:
        print(f"{abrv} \t ({abrv.start}, {abrv.end}) {abrv._.long_form}")
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ pip list|grep scispacy
scispacy           0.5.1
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ pip list|grep en_core_sci
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ pip list|grep en_core_sci*
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ python -V
Python 3.9.15
(vega_scispacy_2) zhangx@pve-gpu:~/a_project/q_vegaPython/000.vega_daily/daily_60_scispacy_demo$ python demo_scispacy.py
Abbreviation     Definition
SBMA     (6, 7) Spinal and bulbar muscular atrophy
SBMA     (33, 34) Spinal and bulbar muscular atrophy
AR       (29, 30) androgen receptor

vegaviazhang commented 1 year ago

Hi, I just copied all of your commands and code exactly and it worked for me. Could you please try again?

Thanks Very much for your help.

allenai / scispacy

Run Sample ERROR. #459

Add the abbreviation pipe to the spacy pipeline.