Missing entry point

[srmeier]

Attempting to try out the example template via below:

docker run -it --entrypoint=/bin/bash -p 5000:5000 asreview/asreview
cd ~
curl https://raw.githubusercontent.com/asreview/systematic-review-datasets/master/datasets/Bos_2018/output/Bos_2018.csv -o Bos_2018.csv
git clone https://github.com/asreview/template-extension-new-model.git
cd template-extension-new-model/
pip install .
cd ..
asreview simulate Bos_2018.csv -m nb_example

Running into the following error:

            _____ _____            _
     /\    / ____|  __ \          (_)
    /  \  | (___ | |__) |_____   ___  _____      __
   / /\ \  \___ \|  _  // _ \ \ / / |/ _ \ \ /\ / /
  / ____ \ ____) | | \ \  __/\ V /| |  __/\ V  V /
 /_/    \_\_____/|_|  \_\___| \_/ |_|\___| \_/\_/

---------------------------------------------------------------------------------
|                                                                                |
|  Welcome to the ASReview Automated Systematic Review software.                 |
|  In this mode the computer will simulate how well the ASReview software        |
|  could have accelerate the systematic review of your dataset.                  |
|  You can sit back and relax while the computer runs this simulation.           |
|                                                                                |
|  GitHub page:        https://github.com/asreview/asreview                      |
|  Questions/remarks:  asreview@uu.nl                                            |
|                                                                                |
---------------------------------------------------------------------------------

Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/asreview/utils.py", line 189, in _model_class_from_entry_point
    return entry_points[method].load()
KeyError: 'nb_example'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/asreview", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/site-packages/asreview/__main__.py", line 38, in main
    entry.load()().execute(sys.argv[2:])
  File "/usr/local/lib/python3.6/site-packages/asreview/entry_points/simulate.py", line 34, in execute
    review_simulate(path, **args_dict)
  File "/usr/local/lib/python3.6/site-packages/asreview/review/factory.py", line 252, in review_simulate
    review(dataset, *args, mode='simulate', **kwargs)
  File "/usr/local/lib/python3.6/site-packages/asreview/review/factory.py", line 235, in review
    reviewer = get_reviewer(*args, mode=mode, model=model, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/asreview/review/factory.py", line 177, in get_reviewer
    random_state=random_state)
  File "/usr/local/lib/python3.6/site-packages/asreview/models/utils.py", line 58, in get_model
    model_class = get_model_class(method)
  File "/usr/local/lib/python3.6/site-packages/asreview/models/utils.py", line 43, in get_model_class
    return _model_class_from_entry_point(method, "asreview.models")
  File "/usr/local/lib/python3.6/site-packages/asreview/utils.py", line 192, in _model_class_from_entry_point
    f"Error: method '{method}' is not implemented for entry point "
ValueError: Error: method 'nb_example' is not implemented for entry point asreview.models.

Is there something I am missing?

[Rensvandeschoot]

Dear @srmeier, thanks for testing this pipeline! Could you upgrade ASReview (+the docker) to the latest version and test again?

[srmeier]

Hi @Rensvandeschoot, Thanks. Updated to latest version but receiving a different error now:

docker run -it --entrypoint=/bin/bash -p 5000:5000 asreview/asreview:latest
cd ~
pip install --upgrade asreview
curl https://raw.githubusercontent.com/asreview/systematic-review-datasets/master/datasets/Bos_2018/output/Bos_2018.csv -o Bos_2018.csv
git clone https://github.com/asreview/template-extension-new-model.git
cd template-extension-new-model/
pip install .
cd ..
asreview simulate Bos_2018.csv -m nb_example

Running into the following:

Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/asreview/utils.py", line 205, in _model_class_from_entry_point
    return entry_points[method].load()
  File "/usr/local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2447, in load
    return self.resolve()
  File "/usr/local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2453, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/usr/local/lib/python3.6/site-packages/asreviewcontrib/models/__init__.py", line 1, in <module>
    from asreviewcontrib.models.nb_default_param import NaiveBayesDefaultParamsModel
  File "/usr/local/lib/python3.6/site-packages/asreviewcontrib/models/nb_default_param.py", line 3, in <module>
    from asreview.models.base import BaseTrainModel
ImportError: cannot import name 'BaseTrainModel'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/asreview", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/site-packages/asreview/__main__.py", line 80, in main
    entry.load()().execute(sys.argv[2:])
  File "/usr/local/lib/python3.6/site-packages/asreview/entry_points/simulate.py", line 47, in execute
    review_simulate(path, **args_dict)
  File "/usr/local/lib/python3.6/site-packages/asreview/review/factory.py", line 330, in review_simulate
    review(dataset, *args, mode='simulate', **kwargs)
  File "/usr/local/lib/python3.6/site-packages/asreview/review/factory.py", line 284, in review
    reviewer = get_reviewer(*args, mode=mode, model=model, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/asreview/review/factory.py", line 204, in get_reviewer
    random_state=random_state)
  File "/usr/local/lib/python3.6/site-packages/asreview/models/classifiers/utils.py", line 63, in get_classifier
    model_class = get_classifier_class(name)
  File "/usr/local/lib/python3.6/site-packages/asreview/models/classifiers/utils.py", line 43, in get_classifier_class
    return _model_class_from_entry_point(name, "asreview.models.classifiers")
  File "/usr/local/lib/python3.6/site-packages/asreview/utils.py", line 212, in _model_class_from_entry_point
    f"Failed to import '{method}' model ({entry_name}) "
ValueError: Failed to import 'nb_example' model (asreview.models.classifiers) with the following error:
cannot import name 'BaseTrainModel'

[J535D165]

Sorry for the inconvenience. It turns out to be an issue with the latest tag of our Docker automated builds. Using the specific tag works (and made a small fix in the template). I will work on a fix.

See the updated code for a working version.

docker run -it --entrypoint=/bin/bash -p 5000:5000 asreview/asreview:release-0.16
cd ~
curl https://raw.githubusercontent.com/asreview/systematic-review-datasets/master/datasets/Bos_2018/output/Bos_2018.csv -o Bos_2018.csv
git clone https://github.com/asreview/template-extension-new-model.git
pip install template-extension-new-model/
asreview algorithms
asreview simulate Bos_2018.csv -m nb_example

[J535D165]

And it might be useful to store your results somewhere.

asreview simulate Bos_2018.csv -m nb_example -s state_bos.h5

[srmeier]

Works perfectly, thanks @J535D165 !