medcat.utils.preprocess_snomed.Snomed - FileNotFoundError

[KeironO]

Hi there,

Whenever I attempt to use the Snomed preprocess utility set, I have file not found errors:

from medcat.utils.preprocess_snomed import Snomed
snomed = Snomed("C:/path/to/dir/uk_sct2cl_32.7.0_20211124000001Z/")
cdf = snomed.to_concept_df()

Returns

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-23-5eb639e435ed> in <module>
----> 1 cdf = snomed.to_concept_df()

~\Projects\nlp\env\lib\site-packages\medcat\utils\preprocess_snomed.py in to_concept_df(self)
     50                     snomed_v = m.group(1)
     51 
---> 52             int_terms = parse_file(f'{contents_path}/sct2_Concept_Snapshot_{snomed_v}_{snomed_release}.txt')
     53             active_terms = int_terms[int_terms.active == '1']
     54             del int_terms

~\Projects\nlp\env\lib\site-packages\medcat\utils\preprocess_snomed.py in parse_file(filename, first_row_header, columns)
      7 
      8 def parse_file(filename, first_row_header=True, columns=None):
----> 9     with open(filename, encoding='utf-8') as f:
     10         entities = [[n.strip() for n in line.split('\t')] for line in f]
     11         return pd.DataFrame(entities[1:], columns=entities[0] if first_row_header else columns)

FileNotFoundError: [Errno 2] No such file or directory: 'C:/path/to/dir/uk_sct2cl_32.7.0_20211124000001Z/SnomedCT_UKClinicalRefsetsRF2_PRODUCTION_20211124T000001Z\\Snapshot\\Terminology/sct2_Concept_Snapshot_INT_20211124.txt'

Where the file is named sct2_Concept_UKCRSnapshot_GB1000000_20211124.txt

Best wishes,

Keiron

[antsh3k]

Dear Keiron,

Thank you for flagging to the team that the format of new UK extension releases has now changed.
I will make changes to enable the processing of the new release format and will let you know when it is done.

[KeironO]

@antsh3k no worries, I can have a go at fixing it if you're snowed under?

[antsh3k]

dw, I can change it. Although, If you can test and feedback that would be amazing!

The changes will be reviewed and integrated by tomorrow.

[antsh3k]

The changes have been made PR #199. The following should work now:
from medcat.utils.preprocess_snomed import Snomed
snomed = Snomed("C:/path/to/dir/uk_sct2cl_32.7.0_20211124000001Z/")
snomed.uk_ext = True # Note: this will only work with UK extensions >2021 with the new release format. Prior UK extension releases should skip this step.
cdf = snomed.to_concept_df()

Let me know if there are any further issues.

[KeironO]

Seems to work fine now. Thank you for your work :D