From ec79ed430ded75ad6befc73de1600e8dc841c7aa Mon Sep 17 00:00:00 2001
From: Carlos Vega <carlos.vega@uni.lu>
Date: Tue, 19 Nov 2019 12:22:43 +0100
Subject: [PATCH] standarise entity codes
---
biokb/biokb.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/biokb/biokb.py b/biokb/biokb.py
index e22c3d4..acbd1c5 100644
--- a/biokb/biokb.py
+++ b/biokb/biokb.py
@@ -2,7 +2,7 @@ from typing import List
from interface.TextMiningService import TextMiningService
from models.publication import Publication
from models.coocurrence import CoOccurrence
-from biokb.utils import uri_to_code
+from utils import uri_to_entity_code, standarise_underscored_entity_code
from SPARQLWrapper import SPARQLWrapper, JSON
from SPARQLWrapper.SPARQLExceptions import EndPointNotFound, EndPointInternalError, QueryBadFormed
@@ -39,6 +39,7 @@ class BioKBservice(TextMiningService):
entity_subquery = ""
for entity in entities:
+ entity = standarise_underscored_entity_code(entity)
entity_subquery += f"?publication <http://lcsb.uni.lu/biokb#containsEntity> <http://lcsb.uni.lu/biokb/entities/{entity}> .\n"
query = """
@@ -59,6 +60,7 @@ class BioKBservice(TextMiningService):
return values
def get_co_occurrences(self, entity: str) -> List[CoOccurrence]:
+ entity = standarise_underscored_entity_code(entity)
query = """
select * where {
@@ -93,7 +95,7 @@ class BioKBservice(TextMiningService):
values = []
values = []
for result in results['results']['bindings']:
- entity_code = uri_to_code(result['other_entity']['value'])
+ entity_code = uri_to_entity_code(result['other_entity']['value'])
count = int(result['count']['value'])
co_occur = CoOccurrence(entity_code, count)
values.append(co_occur)
--
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