Error import umls

[Hamico]

Hi Jiba,
I have the follower error:
return codecs.charmap_decode(input,self.errors,decoding_table)[0]
UnicodeDecodeError: ‘charmap’ can’t decode byte 0x81 in position 5439: character maps to <undefined>

How can I solve the problem?
Many thanks.
Best regards,
Hamico

[Jiba]

Hi,

UMLS files are normally encoded in ASCII, so there is no decoding required.

Could you give me the entire traceback, to investigate the problem?

Thank you,
Jiba

[Hamico]

Hi Jiba,
My full output is the follower:

* Owlready2 * Warning: optimized Cython parser module 'owlready2_optimized' is not available, defaulting to slower Python implementation
Importing UMLS from Zip file 2018AB-full/2018ab-1-meta.nlm...
  Parsing 2018AB/META/MRRANK.RRF.gz as MRRANK...
Traceback (most recent call last):
  File "C:/Users/developer/PycharmProjects/Prova/Script5.py", line 5, in <module>
    import_umls("umls-2018AB-full.zip", terminologies = ["ICD10", "SNOMEDCT_US", "CUI"])
  File "C:\Users\developer\PycharmProjects\Prova\venv\lib\site-packages\owlready2\pymedtermino2\umls.py", line 682, in import_umls
  Parsing 2018AB/META/MRCONSO.RRF.aa.gz as MRCONSO...
    remnants[table_name])
  File "C:\Users\developer\PycharmProjects\Prova\venv\lib\site-packages\owlready2\pymedtermino2\umls.py", line 79, in parse_mrconso
    for line in f:
  File "C:\Users\developer\AppData\Local\Programs\Python\Python37\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 0x81 in position 5439: character maps to <undefined>




How can I solve the error?
Many thanks.

Hamico

[Jiba]

Hi,

It seems that your computer does not use UTF-8 as default encoding.

I fixed UMLS importation to force UTF-8 encoding, in the development version.

Could you try again with this new version?

Jiba

[Hamico]

Hi Jiba,
It works. The file has a size of 2,3 GB.

Many thanks.
Best regards,
Hamico