java.lang.ClassNotFoundException: edu.stanford.nlp.pipeline.StanfordCoreNLPServer

[nondefo]

Error: Could not find or load main class edu.stanford.nlp.pipeline.StanfordCoreNLPServer Caused by: java.lang.ClassNotFoundException: edu.stanford.nlp.pipeline.StanfordCoreNLPServer . . . when trying to run command: java -mx6g -cp "./rule_based/parser/*" edu.stanford.nlp.pipeline.StanfordCoreNLPServer -port 10000 -timeout 30000

[OIELILLIE]

Place the contents of the directory "stanford-corenlp-full-2018-10-05", extracted from the parser downloaded in Step 7, into ./rule_based/parser/

[nondefo]

Hi there,

Thanks for the quick response. The server is running. But now I am this command on a separate terminal:

python3 ./learning_based/paralleloie.py -i data/pubmedabstracts.json

And I get this response:

**Initializing Parallel Triple Extraction. Loading dependencies and dataset...

Traceback (most recent call last):

File "./learning_based/paralleloie.py", line 35, in

from allennlp.predictors.predictor import Predictor

File "/usr/local/lib/python3.7/site-packages/allennlp/predictors/init.py", line 9, in

from allennlp.predictors.predictor import Predictor

File "/usr/local/lib/python3.7/site-packages/allennlp/predictors/predictor.py", line 12, in

from allennlp.data import DatasetReader, Instance

File "/usr/local/lib/python3.7/site-packages/allennlp/data/init.py", line 1, in

from allennlp.data.dataset_readers.dataset_reader import DatasetReader

File "/usr/local/lib/python3.7/site-packages/allennlp/data/dataset_readers/init.py", line 10, in

from allennlp.data.dataset_readers.ccgbank import CcgBankDatasetReader

File "/usr/local/lib/python3.7/site-packages/allennlp/data/dataset_readers/ccgbank.py", line 9, in

from allennlp.data.dataset_readers.dataset_reader import DatasetReader

File "/usr/local/lib/python3.7/site-packages/allennlp/data/dataset_readers/dataset_reader.py", line 8, in

from allennlp.data.instance import Instance

File "/usr/local/lib/python3.7/site-packages/allennlp/data/instance.py", line 3, in

from allennlp.data.fields.field import DataArray, Field

File "/usr/local/lib/python3.7/site-packages/allennlp/data/fields/init.py", line 7, in

from allennlp.data.fields.array_field import ArrayField

File "/usr/local/lib/python3.7/site-packages/allennlp/data/fields/array_field.py", line 10, in

class ArrayField(Field[numpy.ndarray]):

File "/usr/local/lib/python3.7/site-packages/allennlp/data/fields/array_field.py", line 50, in ArrayField

@overrides

File "/usr/local/lib/python3.7/site-packages/overrides/overrides.py", line 88, in overrides

return _overrides(method, check_signature, check_at_runtime)

File "/usr/local/lib/python3.7/site-packages/overrides/overrides.py", line 114, in _overrides

_validate_method(method, super_class, check_signature)

File "/usr/local/lib/python3.7/site-packages/overrides/overrides.py", line 135, in _validate_method

ensure_signature_is_compatible(super_method, method, is_static)

File "/usr/local/lib/python3.7/site-packages/overrides/signature.py", line 93, in ensure_signature_is_compatible

ensure_return_type_compatibility(super_type_hints, sub_type_hints, method_name)

File "/usr/local/lib/python3.7/site-packages/overrides/signature.py", line 288, in ensure_return_type_compatibility

f"{method_name}: return type `{sub_return}` is not a `{super_return}`."

TypeError: ArrayField.empty_field: return type None is not a <class 'allennlp.data.fields.field.Field'>.**

It doesn't seem like anything from my side. Could you let me know what the issue could be?

[OIELILLIE]

Try: pip install overrides==3.1.0

[nondefo]

For this command:

python3 ./learning_based/paralleloie.py -i data/pubmedabstracts.json

I eventually get an error:

Initializing Parallel Triple Extraction. Loading dependencies and dataset... Done Coreference resolution in progress... 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 38869/38869 [3:11:42<00:00, 3.38it/s] Done Triple extraction in progress... 0it [00:00, ?it/s] Traceback (most recent call last): File "./learning_based/paralleloie.py", line 130, in sent_text = nltk.sent_tokenize(text) File "/usr/local/lib/python3.7/site-packages/nltk/tokenize/init.py", line 105, in sent_tokenize tokenizer = load('tokenizers/punkt/{0}.pickle'.format(language)) File "/usr/local/lib/python3.7/site-packages/nltk/data.py", line 868, in load opened_resource = _open(resource_url) File "/usr/local/lib/python3.7/site-packages/nltk/data.py", line 993, in open return find(path, path + ['']).open() File "/usr/local/lib/python3.7/site-packages/nltk/data.py", line 701, in find raise LookupError(resource_not_found) LookupError:

---

Resource punkt not found. Please use the NLTK Downloader to obtain the resource:

import nltk nltk.download('punkt')

For more information see: https://www.nltk.org/data.html

Attempted to load tokenizers/punkt/PY3/english.pickle

Searched in:

• '/Users/nony/nltk_data'
• '/usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/nltk_data'
• '/usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/share/nltk_data'
• '/usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/lib/nltk_data'
• '/usr/share/nltk_data'
• '/usr/local/share/nltk_data'
• '/usr/lib/nltk_data'
• '/usr/local/lib/nltk_data'
• ''

  ---

[OIELILLIE]

$ python3 >>> import nltk >>> nltk.download("punkt")

[nondefo]

Thanks!

The final command: python3 ./rule_based/extract_refine.py -i extracted_triples_learning.csv

Returns:

[nltk_data] Downloading package stopwords to /Users/nony/nltk_data... [nltk_data] Package stopwords is already up-to-date! Traceback (most recent call last): File "./rule_based/extract_refine.py", line 361, in inp = parser.parse_args().infile NameError: name 'parser' is not defined

[OIELILLIE]

Change line 361 of ./rule_based/extract_refine.py to: inp = ap.parse_args().infile

[nondefo]

Still getting an error :

[nltk_data] Downloading package stopwords to /Users/nony/nltk_data... [nltk_data] Package stopwords is already up-to-date! Traceback (most recent call last): File "./rule_based/extract_refine.py", line 366, in [(ln["subject"],ln["predicate"],ln["object"])]) TypeError: 'NoneType' object is not subscriptable

[nondefo]

Ok, the triples have been extracted, thanks.