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update phenopy api #43

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update phenopy api #43

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ca4ad7d
update phenopy api
arvkevi Jan 5, 2021
21fd929
handle gensim 3.8 and 4.0
arvkevi Jan 6, 2021
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7 changes: 6 additions & 1 deletion txt2hpo/nlp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,12 @@ def similarity_term_to_context(term, context, model):
:return: float
"""
def remove_out_of_vocab(tokens):
return [x for x in tokens if x in model.key_to_index]
try:
# gensim 3.8
return [x for x in tokens if x in model.vocab]
except AttributeError:
# gensim 4.0
return [x for x in tokens if x in model.wv.key_to_index]

hpo_term = hpo_network.nodes[term]
hpo_term_definition = hpo_term['name']
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2 changes: 1 addition & 1 deletion txt2hpo/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

import math
from phenopy.config import config as phenopy_config
from phenopy import generate_annotated_hpo_network
from phenopy.build_hpo import generate_annotated_hpo_network

import sys
import subprocess
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