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Georgetown-IR-Lab / QuickUMLS

System for Medical Concept Extraction and Linking
MIT License
369 stars 95 forks source link

install quickUMLS #84

Open om35 opened 2 years ago

om35 commented 2 years ago

hello how are you, I tried to install this version with preferred term but i have this problem when installing it

File "C:\Users\ouerf\anaconda4\lib\site-packages\setuptools\command\easy_install.py", line 1158, in run_setup run_setup(setup_script, args) File "C:\Users\ouerf\anaconda4\lib\site-packages\setuptools\sandbox.py", line 262, in run_setup raise File "C:\Users\ouerf\anaconda4\lib\contextlib.py", line 131, in exit self.gen.throw(type, value, traceback) File "C:\Users\ouerf\anaconda4\lib\site-packages\setuptools\sandbox.py", line 198, in setup_context yield File "C:\Users\ouerf\anaconda4\lib\contextlib.py", line 131, in exit self.gen.throw(type, value, traceback) File "C:\Users\ouerf\anaconda4\lib\site-packages\setuptools\sandbox.py", line 169, in save_modules saved_exc.resume() File "C:\Users\ouerf\anaconda4\lib\site-packages\setuptools\sandbox.py", line 143, in resume raise exc.with_traceback(self._tb) File "C:\Users\ouerf\anaconda4\lib\site-packages\setuptools\sandbox.py", line 156, in save_modules yield saved File "C:\Users\ouerf\anaconda4\lib\site-packages\setuptools\sandbox.py", line 198, in setup_context yield File "C:\Users\ouerf\anaconda4\lib\site-packages\setuptools\sandbox.py", line 259, in run_setup _execfile(setup_script, ns) File "C:\Users\ouerf\anaconda4\lib\site-packages\setuptools\sandbox.py", line 46, in _execfile exec(code, globals, locals) File "C:\Users\ouerf\AppData\Local\Temp\easy_install-asoev6ao\quickumls_simstring-1.1.5r1\setup.py", line 93, in File "C:\Users\ouerf\anaconda4\lib\encodings\cp1252.py", line 23, in decode return codecs.charmap_decode(input,self.errors,decoding_table)[0] UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position 471: character maps to

sonalkum commented 1 year ago

@om35 I am also facing similar issue, were you able to find any resolution?

soldni commented 1 year ago

I would recommend running QuickUMLS on WSL

sonalkum commented 1 year ago

@soldni Thanks for the heads up, it worked.

abishek85 commented 1 year ago

@soldni The problem is that the Readme file for quickumls-simstring was probably saved from linux and encoded using utf-8. When the setup.py tries to read it on windows, it throws an error. I was able to get past this error by modifying quickumls-simstring setup.py Line 92 from:

with open('README.md') as reader:

to:

with open('README.md','r',encoding='utf-8') as reader: