Fresh QuickUMLS installation on Windows 10 returning empty [] - no errors

[khankanz]

Describe the bug

• running test script following fresh Windows installation returns []

Environment

• conda env with python 3.8.10, quickumls 1.4.0.post1, quickumls-simstring 1.1.5r2
• Windows 10

Additional context

• followed the installation guide. Ran into issues with simstring installation but was able to resolve following the steps from /Georgetown-IR-Lab/simstring)
• had to update core.py to load spacy with: self.nlp = spacy.load('en_core_web_sm')
• the following test script returns []:
• from quickumls import QuickUMLS matcher = QuickUMLS(quickumls_fp='FILEPATH TO QUICKUMLS') text = "The ulna has dislocated posteriorly from the trochlea of the humerus." print(matcher.match(text, best_match=True, ignore_syntax=False))

[khankanz]

Happy to provide additional details. Not sure which direction to investigate further.

[khankanz]

I started to dig into the source code. I started writing scripts to test pieces of the code. I'm noticing that the retrieve function keeps returning null. This same script works perfectly fine on my Ubuntu VM.

import unicodedata
from quickumls_simstring import simstring
import os, six, unicodedata

def safe_unicode(s):
    if six.PY2:
        # in python 3, there no ambiguity on whether
        # a string is encoded in bytes format or not
        try:
            s = u'%s' % s
        except UnicodeDecodeError:
            s = u'%s' % s.decode('utf-8')

    return u'{}'.format(unicodedata.normalize('NFKD', s))

def prepare_string_for_db_input(s):
    if six.PY2:
        print('s > six.PY2', s)
        return s.encode('utf-8')
    else:
        print('s > NO six.PY2', s)
        return s

path = "FILEPATH/umls-simstring.db"
print(os.path.join(path, 'umls-terms.simstring'))
db = simstring.reader(os.path.join(path, 'umls-terms.simstring'))
#Use cosine & threshold 0.6
db.measure = simstring.cosine
db.threshold = 0.6
term = "elbow, ula"

print('term ready for db lookup:', prepare_string_for_db_input(safe_unicode(term)))
print(db.retrieve(prepare_string_for_db_input(safe_unicode(term))))