Example code couldn't run

[albert-ying]

Got import error at begining

[albert-ying]

And also got bunch of undefined error at p_53 function.

[albert-ying]

I think you may forgot to push something when updating the release

[dmalzl]

I had a similar problem and I think this is because the download links to the SPECIALIST lexicon are outdated
I think it should work if you update the urls in the lex_file_to_url.json to something like this https://data.lhncbc.nlm.nih.gov/public/lsg/lexicon/2023/release/LEX_DOC/*
see here for other versions

[dmalzl]

Okay sorry this is not the reason but yet another issue. These things should actually be in the map_sra_to_ontology module but seem to not be imported correctly

[dmalzl]

okay so most of what is needed is in the map_sra_to_ontology/pipeline_components.py file. So you need to import everything from this as well as import SpecialistLexicon from map_sra_to_ontology/load_specialist_lex.py. Additionally you might also need to run:

import nltk
nltk.download('punkt')

to download the tokenizer data for nltk

[dmalzl]

you can also checkout the run_pipeline.py file from my fork of the repo here