new install attempt with SNOMED model throws spacy/thinc config validation error about medcat HOT 4 CLOSED

To answer my own question, I did the other suggested example in the tutorial, and added an extra couple lines to fix that issue:

from medcat.vocab import Vocab
from medcat.cdb import CDB
from medcat.cat import CAT
from medcat.meta_cat import MetaCAT

unzip = '<path>/mc_modelpack_snomed_int_16_mar_2022_25be3857ba34bdd5/'
# Load the vocab model you downloaded
vocab = Vocab.load(unzip+'vocab.dat')
# Load the cdb model you downloaded
cdb = CDB.load(unzip+'cdb.dat')

#needed to add these two lines
cdb.config.linking.filters.cuis = set()
cdb.config.general.spacy_model = unzip+'spacy_model'

# Download the mc_status model from the models section below and unzip it
mc_status = MetaCAT.load(unzip+'meta_Status/')
cat = CAT(cdb=cdb, config=cdb.config, vocab=vocab, meta_cats=[mc_status])

from medcat.

@ryleyb , I ran into the same problem with medcat==1.7.0 and can confirm that your solution resolved it.

from medcat.

The problem is the fact that the model you guys are trying to run is from medcat v1.2. However, version 1.3 introduced some changes (mostly to do with data validation) that mean the default of {} (which is parsed as a dictionary) is not correct where a set is expected.

I've created a PR (#313) that will allow one to fix the issue for a model pack without in-code manual intervention.

from medcat.

The problem also occured for me today but using this code snipppet also fixed it for me.

To answer my own question, I did the other suggested example in the tutorial, and added an extra couple lines to fix that issue:

from medcat.vocab import Vocab
from medcat.cdb import CDB
from medcat.cat import CAT
from medcat.meta_cat import MetaCAT

unzip = '<path>/mc_modelpack_snomed_int_16_mar_2022_25be3857ba34bdd5/'
# Load the vocab model you downloaded
vocab = Vocab.load(unzip+'vocab.dat')
# Load the cdb model you downloaded
cdb = CDB.load(unzip+'cdb.dat')

#needed to add these two lines
cdb.config.linking.filters.cuis = set()
cdb.config.general.spacy_model = unzip+'spacy_model'

# Download the mc_status model from the models section below and unzip it
mc_status = MetaCAT.load(unzip+'meta_Status/')
cat = CAT(cdb=cdb, config=cdb.config, vocab=vocab, meta_cats=[mc_status])

from medcat.