From 56af3cda230d312dfc67322cc0ffb8fb8aded4e3 Mon Sep 17 00:00:00 2001
From: James Brandreth <30596689+jamesbrandreth@users.noreply.github.com>
Date: Thu, 19 Sep 2024 14:00:07 +0100
Subject: [PATCH] fix: start numbering concepts from 1 (#126)

* fix: start numbering concepts from 1

* update numbers in tests
---
 src/miade/annotators.py | 4 ++--
 tests/test_core.py      | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/miade/annotators.py b/src/miade/annotators.py
index 1b7e1e5..c80c504 100644
--- 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
index 61eb14e..115be33 100644
--- 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,