diff --git a/biokb/biokb.py b/biokb/biokb.py index baa460084862c338590540951c903f03599bf616..e22c3d4f52615042a865684be676a64cc47c84b1 100644 --- a/biokb/biokb.py +++ b/biokb/biokb.py @@ -10,6 +10,7 @@ from SPARQLWrapper.SPARQLExceptions import EndPointNotFound, EndPointInternalErr import logging logger = logging.getLogger(__name__) + class BioKBClientException(Exception): pass @@ -93,7 +94,7 @@ class BioKBservice(TextMiningService): values = [] for result in results['results']['bindings']: entity_code = uri_to_code(result['other_entity']['value']) - count = int(result['count']['value']) - co_occur = CoOccurrence(entity_code, count) + count = int(result['count']['value']) + co_occur = CoOccurrence(entity_code, count) values.append(co_occur) return values diff --git a/biokb/utils.py b/biokb/utils.py index 41ec42151f36dfa97b4f7539534f80c288a9e7f1..092c7926ce7179636392e8494de577fd69bf5cb7 100644 --- a/biokb/utils.py +++ b/biokb/utils.py @@ -1,10 +1,10 @@ def uri_to_code(uri: str) -> str: """Translates URIs such as http://lcsb.uni.lu/biokb/entities/BTO_0001043 to BTO_0001043 - + Arguments: uri {str} -- [description] - + Returns: str -- [description] """ - return uri.split('/')[-1] \ No newline at end of file + return uri.split('/')[-1] diff --git a/interface/TextMiningService.py b/interface/TextMiningService.py index f2b07c61d13ca95213e44de176bfc5f50cbe5a2b..b5237e25735e769a8de430c6dba94b1b3a55a1ff 100644 --- a/interface/TextMiningService.py +++ b/interface/TextMiningService.py @@ -3,6 +3,7 @@ from typing import List from models.publication import Publication from models.coocurrence import CoOccurrence + class TextMiningService(metaclass=ABCMeta): def __init__(self, name: str, description: str): diff --git a/models/coocurrence.py b/models/coocurrence.py index 3dc0f8c9dcaa6ef25f43b45ee711d0cf4f50ed2d..8d4384e41c329276690d91f3ba10950f320bff55 100644 --- a/models/coocurrence.py +++ b/models/coocurrence.py @@ -1,4 +1,4 @@ class CoOccurrence: def __init__(self, entity: str, score: float): self.entity = entity - self.score = score \ No newline at end of file + self.score = score diff --git a/models/publication.py b/models/publication.py index 84c2685e1a0750515f7741dff7ca354c169ebcd0..43d39bb4db6cf13e5e5234cd74fb7a2cd4f4239f 100644 --- a/models/publication.py +++ b/models/publication.py @@ -4,4 +4,4 @@ class Publication: self.pm_id = pm_id self.doi = doi self.preprint_id = preprint_id - self.other_id = other_id \ No newline at end of file + self.other_id = other_id