fix: start numbering concepts from 1 (#126)

* fix: start numbering concepts from 1 * update numbers in tests
uclh-criu · Sep 19, 2024 · 56af3cd · 56af3cd
1 parent 77dfb39
commit 56af3cd
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/src/miade/annotators.py b/src/miade/annotators.py
@@ -488,9 +488,9 @@ def add_numbering_to_name(concepts: List[Concept]) -> List[Concept]:
  Returns:
  The list of concepts with numbering added to their names.
  """
- # Prepend numbering to problem concepts e.g. 00 asthma, 01 stroke...
+ # Prepend numbering to problem concepts e.g. 01 asthma, 02 stroke...
  for i, concept in enumerate(concepts):
- concept.name = f"{i:02} {concept.name}"
+ concept.name = f"{(i+1):02} {concept.name}"
 
  return concepts
 

diff --git a/tests/test_core.py b/tests/test_core.py
@@ -15,19 +15,19 @@ def test_core(model_directory_path, test_note, test_negated_note, test_duplicate
  processor.add_annotator("meds/allergies")
 
  assert processor.process(test_note) == [
- Concept(id="59927004", name="00 liver failure", category=Category.PROBLEM),
+ Concept(id="59927004", name="01 liver failure", category=Category.PROBLEM),
  Concept(id="322236009", name="paracetamol 500mg oral tablets", category=Category.MEDICATION),
  ]
  assert processor.process(test_negated_note) == [
  Concept(id="322236009", name="paracetamol 500mg oral tablets", category=Category.MEDICATION),
  ]
  assert processor.process(test_duplicated_note) == [
- Concept(id="59927004", name="00 liver failure", category=Category.PROBLEM),
+ Concept(id="59927004", name="01 liver failure", category=Category.PROBLEM),
  Concept(id="322236009", name="paracetamol 500mg oral tablets", category=Category.MEDICATION),
  ]
  assert processor.get_concept_dicts(test_note) == [
  {
- "name": "00 liver failure",
+ "name": "01 liver failure",
  "id": "59927004",
  "category": "PROBLEM",
  "start": 12,