From cc5f8f125425ca81322f32df9451fad26d76dfcf Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 22 Apr 2022 17:09:47 -0400 Subject: [PATCH 1/2] Fixed typo in Scigraph API call `include_abbrev` -> `includeAbbrev`, as per https://scigraph-ontology.monarchinitiative.org/scigraph/docs/#operations,post-/annotations/entities,annotations --- biolink/api/nlp/endpoints/annotate.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/biolink/api/nlp/endpoints/annotate.py b/biolink/api/nlp/endpoints/annotate.py index db749c1..dd1cb8c 100644 --- a/biolink/api/nlp/endpoints/annotate.py +++ b/biolink/api/nlp/endpoints/annotate.py @@ -39,7 +39,7 @@ def parse_args_for_annotator(parser): args['longestOnly'] = val if 'include_abbreviation' in args: val = args.pop('include_abbreviation') - args['include_abbrev'] = val + args['includeAbbrev'] = val if 'include_acronym' in args: val = args.pop('include_acronym') args['includeAcronym'] = val From 1dfffb646bd06cdeff060b1776a11404cef2fdc0 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 22 Apr 2022 17:12:42 -0400 Subject: [PATCH 2/2] Removed duplicate `include_acronym` processing --- biolink/api/nlp/endpoints/annotate.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/biolink/api/nlp/endpoints/annotate.py b/biolink/api/nlp/endpoints/annotate.py index dd1cb8c..0be9c9c 100644 --- a/biolink/api/nlp/endpoints/annotate.py +++ b/biolink/api/nlp/endpoints/annotate.py @@ -43,9 +43,6 @@ def parse_args_for_annotator(parser): if 'include_acronym' in args: val = args.pop('include_acronym') args['includeAcronym'] = val - if 'include_acronym' in args: - val = args.pop('include_acronym') - args['includeAcronym'] = val if 'include_numbers' in args: val = args.pop('include_numbers') args['includeNumbers'] = val