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stanfordmlgroup / chexpert-labeler

CheXpert NLP tool to extract observations from radiology reports.
MIT License
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Import error with bllipparser/_CharniakParser.so #3

Closed tobiolatunji closed 5 years ago

tobiolatunji commented 5 years ago

Hi. I've followed the instructions for the NegBio install. Everything works fine till step 5 where I get an import error.

Download the GENIA+PubMed parsing model: >>> from bllipparser import RerankingParser >>> RerankingParser.fetch_and_load('GENIA+PubMed')

Full traceback

Traceback (most recent call last): File "", line 1, in File "/anaconda3/envs/negbio2.7/lib/python2.7/site-packages/bllipparser/init.py", line 399, in from .RerankingParser import RerankingParser, Tree, Sentence, tokenize File "/anaconda3/envs/negbio2.7/lib/python2.7/site-packages/bllipparser/RerankingParser.py", line 19, in from . import CharniakParser as parser File "/anaconda3/envs/negbio2.7/lib/python2.7/site-packages/bllipparser/CharniakParser.py", line 28, in _CharniakParser = swig_import_helper() File "/anaconda3/envs/negbio2.7/lib/python2.7/site-packages/bllipparser/CharniakParser.py", line 24, in swig_import_helper _mod = imp.load_module('_CharniakParser', fp, pathname, description) ImportError: dlopen(/anaconda3/envs/negbio2.7/lib/python2.7/site-packages/bllipparser/_CharniakParser.so, 2): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv Referenced from: /anaconda3/envs/negbio2.7/lib/python2.7/site-packages/bllipparser/_CharniakParser.so Expected in: /usr/lib/libstdc++.6.dylib in /anaconda3/envs/negbio2.7/lib/python2.7/site-packages/bllipparser/_CharniakParser.so

Seems it's some issue with how the package is compiled?

Mac Version 10.14, Anaconda3

alistairewj commented 5 years ago

Do you have XCode installed? At a guess it's trying to import a library that doesn't exist.

tobiolatunji commented 5 years ago

Yep, installed Xcode. Still fails. I switched to Linux and it installed fine.

tobiolatunji commented 5 years ago

New problem though, still with bllipparser.

(chexpert-label) /////projects/chexpert-labeler$ python Python 3.6.7 |Anaconda, Inc.| (default, Oct 23 2018, 19:16:44) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.

from bllipparser import RerankingParser RerankingParser.fetch_and_load('GENIA+PubMed') Error downloading model (501 Not Implemented)

tobiolatunji commented 5 years ago

Error looks like it's coming from the bllipparser model downloader.

from bllipparser import RerankingParser rrp = RerankingParser.fetch_and_load('WSJ-PTB3', verbose=True) Model directory: /home/tobi/.local/share/bllipparser/WSJ-PTB3 Fetching model: WSJ-PTB3 from https://www.dropbox.com/s/ulcfs7my1ifriuu/BLLIP-WSJ-PTB3.tar.bz2?dl=1 Error downloading model (501 Not Implemented)

alistairewj commented 5 years ago

Are you behind a proxy? I think that might mess up the bllip parser download code. You should probably post this issue on their repo.

As a workaround, you could try downloading the compressed archive from that DropBox link yourself and extracting it into the ~/.local/share/bllipparser/GENIA+PubMed/ folder.

tobiolatunji commented 5 years ago

That worked. Thank you!!