strange error occur, when I run python negbio/main_chexpert.py text --output=examples/test.neg.xml examples/00019248.txt examples/00000086.txt

[bliu62]

{'--bllip-model': '~/.local/share/bllipparser/GENIA+PubMed',
'--mention_phrases_dir': 'negbio/chexpert/phrases/mention',
'--neg-patterns': 'negbio/chexpert/patterns/negation.txt',
'--newline_is_sentence_break': False,
'--output': 'examples/test.neg.xml',
'--post-negation-uncertainty-patterns': 'negbio/chexpert/patterns/post_negation_uncertainty.txt',
'--pre-negation-uncertainty-patterns': 'negbio/chexpert/patterns/pre_negation_uncertainty.txt',
'--split-document': False,
'--unmention_phrases_dir': 'negbio/chexpert/phrases/unmention',
'--verbose': False,
'SOURCE': None,
'SOURCES': ['examples/00019248.txt', 'examples/00000086.txt'],
'bioc': False,
'text': True}
/home/bo/.local/lib/python3.6/site-packages
/home/bo/.local/lib/python3.6/site-packages
/home/bo/.local/lib/python3.6/site-packages
/home/bo/.local/lib/python3.6/site-packages
/home/bo/.local/lib/python3.6/site-packages
/home/bo/conda/envs/negbio/lib/python3.6/site-packages/StanfordDependencies/JPypeBackend.py:160: UserWarning: This jar doesn't support universal dependencies, falling back to Stanford Dependencies. To suppress this message, call with universal=False
warnings.warn("This jar doesn't support universal "
ERROR:root:Cannot process sentence 0 in 00019248
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String
ERROR:root:Cannot process sentence 72 in 00019248
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String
ERROR:root:Cannot process sentence 123 in 00019248
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String
ERROR:root:Cannot process sentence 142 in 00019248
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String
ERROR:root:Cannot process sentence 201 in 00019248
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String
ERROR:root:Cannot process sentence 0 in 00000086
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String
ERROR:root:Cannot process sentence 73 in 00000086
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String
ERROR:root:Cannot process sentence 94 in 00000086
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String
ERROR:root:Cannot process sentence 122 in 00000086
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String
ERROR:root:Cannot process sentence 139 in 00000086
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String
ERROR:root:Cannot process sentence 204 in 00000086
Traceback (most recent call last):
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 120, in convert_doc
has_lemmas=self._backend == 'jpype')
File "/home/bo/.local/lib/python3.6/site-packages/negbio/pipeline/ptb2ud.py", line 171, in convert_dg
index = text.find(node_form, start)
TypeError: must be str, not java.lang.String

[karanbajaj]

I ran in to the same thing -
I am not a python programmer - But here is my explanation. I think it's the python version issue. After googling and stack overflow it seems that the java objects have to be casted with str().
I have made a few changes on my fork to make it work.