Comments (4)
alexmloveless
commented on July 29, 2024
1
This breaks for Python 2.7 too. Pickle has no arguments on 2.x
$ /usr/local/anaconda2/bin/python cliner predict --txt data/examples/ex_doc.txt --out data/predictions --model models/silver.crf --format i2b2
Traceback (most recent call last):
File "cliner", line 60, in
main()
File "cliner", line 52, in main
predict.main()
File "/data/CliNER-master/code/predict.py", line 79, in main
predict(files, args.model, args.output, format=format)
File "/data/CliNER-master/code/predict.py", line 96, in predict
model = pickle.load(f,encoding = 'latin1')
TypeError: load() got an unexpected keyword argument 'encoding'
Removing the encoding argument results in a different error (same command):
File "/data/CliNER-master/code/machine_learning/crf.py", line 181, in predict
clf_byte = bytearray(clf, 'latin1')
UnicodeDecodeError: 'ascii' codec can't decode byte 0xf4 in position 6: ordinal not in range(128)
I'm not sure if this is a fault with the code or the encoding in the silver.crf pickle.
EDIT:
Temporary workaround. Remove the encoding as above, then on line 181 of code/machine_learning/crf.py remove the encoding from the bytearray() arguments:
before:
clf_byte = bytearray(clf, 'latin1')
after:
clf_byte = bytearray(clf)
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suryacaprice
commented on July 29, 2024
1
same here issue is still there
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simius
commented on July 29, 2024
Changes to model.py, predict.py, and crf.py have been to address the encoding issues.
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rajgupt
commented on July 29, 2024
@simthyrearch - for python 3.7 this issue is still there.
(cliner) C:\Users\rgupta98\github\CliNER\code>python
Python 3.7.1 (default, Dec 10 2018, 22:54:23) [MSC v.1915 64 bit (AMD64)] :: Anaconda, Inc. on win32
Type "help", "copyright", "credits" or "license" for more information.
>>>
(cliner) C:\Users\rgupta98\github\CliNER\code>python ..\cliner predict --txt ../data/examples/ex_doc.txt --out ../data/p
redictions --model ../models/silver.crf --format i2b2
Traceback (most recent call last):
File "..\cliner", line 60, in <module>
main()
File "..\cliner", line 52, in main
predict.main()
File "C:\Users\rgupta98\github\CliNER\code\predict.py", line 79, in main
predict(files, args.model, args.output, format=format)
File "C:\Users\rgupta98\github\CliNER\code\predict.py", line 96, in predict
model = pickle.load(f, encoding='utf8')
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf4 in position 6: invalid continuation byte
(cliner) C:\Users\rgupta98\github\CliNER\code>python ..\cliner predict --txt ../data/examples/ex_doc.txt --out ../data/p
redictions --model ../models/silver.crf --format i2b2
C:\Users\rgupta98\AppData\Local\Continuum\anaconda3\envs\cliner\lib\site-packages\sklearn\base.py:251: UserWarning: Tryi
ng to unpickle estimator DictVectorizer from version 0.19.1 when using version 0.20.1. This might lead to breaking code
or invalid results. Use at your own risk.
UserWarning)
1 of 1
../data/examples/ex_doc.txt
vectorizing words all
predicting labels all
Traceback (most recent call last):
File "..\cliner", line 60, in <module>
main()
File "..\cliner", line 52, in main
predict.main()
File "C:\Users\rgupta98\github\CliNER\code\predict.py", line 79, in main
predict(files, args.model, args.output, format=format)
File "C:\Users\rgupta98\github\CliNER\code\predict.py", line 179, in predict
labels = model.predict_classes_from_document(note)
File "C:\Users\rgupta98\github\CliNER\code\model.py", line 282, in predict_classes_from_document
return self.predict_classes(tokenized_sents)
File "C:\Users\rgupta98\github\CliNER\code\model.py", line 313, in predict_classes
hyperparams = hyperparams)
File "C:\Users\rgupta98\github\CliNER\code\model.py", line 707, in generic_predict
predictions = crf.predict(clf, X)
File "C:\Users\rgupta98\github\CliNER\code\machine_learning\crf.py", line 181, in predict
clf_byte = bytearray(clf)
TypeError: string argument without an encoding
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