Remove debug logging

uclh-criu · Nov 30, 2023 · 17cf7ed · 17cf7ed
1 parent 6eab644
commit 17cf7ed
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git 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
@@ -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),