From 17cf7ed6c5f451a3dd91fe54dc21ff8e5553b507 Mon Sep 17 00:00:00 2001 From: jenniferajiang Date: Thu, 30 Nov 2023 10:45:01 +0000 Subject: [PATCH] Remove debug logging --- src/miade/annotators.py | 1 - tests/conftest.py | 10 +++++----- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/src/miade/annotators.py b/src/miade/annotators.py index 5d18153..f0001a5 100644 --- a/src/miade/annotators.py +++ b/src/miade/annotators.py @@ -19,7 +19,6 @@ from .utils.annotatorconfig import AnnotatorConfig log = logging.getLogger(__name__) -log.setLevel(logging.DEBUG) # Precompile regular expressions sent_regex = re.compile(r"[^\s][^\n]+") diff --git a/tests/conftest.py b/tests/conftest.py index 0b9b252..6818025 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -569,25 +569,25 @@ def test_meds_allergy_note() -> Note: def test_substance_concepts_with_meta_anns() -> List[Concept]: return [ Concept(id="226021002", name="Eggs", start=14, end=17, meta_anns=[ - MetaAnnotations(name="reactionpos", value=ReactionPos.NOT_REACTION), + MetaAnnotations(name="reaction_pos", value=ReactionPos.NOT_REACTION), MetaAnnotations(name="category", value=SubstanceCategory.ADVERSE_REACTION), MetaAnnotations(name="allergy_type", value=AllergyType.INTOLERANCE), MetaAnnotations(name="severity", value=Severity.MILD), ]), Concept(id="159002", name="Penicillin", start=64, end=73, meta_anns=[ - MetaAnnotations(name="reactionpos", value=ReactionPos.NOT_REACTION), + MetaAnnotations(name="reaction_pos", value=ReactionPos.NOT_REACTION), MetaAnnotations(name="category", value=SubstanceCategory.ADVERSE_REACTION), MetaAnnotations(name="allergy_type", value=AllergyType.ALLERGY), MetaAnnotations(name="severity", value=Severity.MODERATE), ]), Concept(id="140004", name="Rash", start=24, end=27, meta_anns=[ - MetaAnnotations(name="reactionpos", value=ReactionPos.AFTER_SUBSTANCE), + MetaAnnotations(name="reaction_pos", value=ReactionPos.AFTER_SUBSTANCE), MetaAnnotations(name="category", value=SubstanceCategory.NOT_SUBSTANCE), MetaAnnotations(name="allergy_type", value=AllergyType.UNSPECIFIED), MetaAnnotations(name="severity", value=Severity.UNSPECIFIED), ]), Concept(id="832007", name="Nausea", start=50, end=55, meta_anns=[ - MetaAnnotations(name="reactionpos", value=ReactionPos.BEFORE_SUBSTANCE), + MetaAnnotations(name="reaction_pos", value=ReactionPos.BEFORE_SUBSTANCE), MetaAnnotations(name="category", value=SubstanceCategory.ADVERSE_REACTION), MetaAnnotations(name="allergy_type", value=AllergyType.UNSPECIFIED), MetaAnnotations(name="severity", value=Severity.UNSPECIFIED), @@ -600,7 +600,7 @@ def test_substance_concepts_with_meta_anns() -> List[Concept]: route=None ), meta_anns=[ - MetaAnnotations(name="reactionpos", value=ReactionPos.NOT_REACTION), + MetaAnnotations(name="reaction_pos", value=ReactionPos.NOT_REACTION), MetaAnnotations(name="category", value=SubstanceCategory.TAKING), MetaAnnotations(name="allergy_type", value=AllergyType.UNSPECIFIED), MetaAnnotations(name="severity", value=Severity.UNSPECIFIED),