working tests for diso/behavior

aphp · Sep 24, 2024 · 4005c96 · 4005c96
1 parent 173bdfc
commit 4005c96
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Showing 16 changed files with 37 additions and 43 deletions.
diff --git a/edsnlp/pipes/ner/behaviors/alcohol/patterns.py b/edsnlp/pipes/ner/behaviors/alcohol/patterns.py
@@ -34,7 +34,7 @@
         ),
         dict(
             name="zero_after",
-            regex=r"(?=^[a-z]*\s*:?[\s-]*(0|non))",
+            regex=r"(?=^[a-z]*\s*:?[\s-]*(0|non|aucun|jamais))",
             window=3,
             reduce_mode="keep_first",
         ),

diff --git a/edsnlp/pipes/ner/behaviors/tobacco/patterns.py b/edsnlp/pipes/ner/behaviors/tobacco/patterns.py
@@ -33,7 +33,7 @@
             ),
             dict(
                 name="zero_after",
-                regex=r"(?=^[a-z]*\s*:?[\s-]*(0|non))",
+                regex=r"(?=^[a-z]*\s*:?[\s-]*(0|non|aucun|jamais))",
                 window=3,
                 reduce_mode="keep_first",
             ),

diff --git a/tests/pipelines/ner/disorders/CKD.py b/tests/pipelines/ner/disorders/CKD.py
@@ -12,7 +12,7 @@
         True,
         False,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=8 * [None] + [{"stage": "IV"}, {"dfg": 30}, None],
     texts=[
         "Patient atteint d'une glomérulopathie.",

diff --git a/tests/pipelines/ner/disorders/COPD.py b/tests/pipelines/ner/disorders/COPD.py
@@ -7,7 +7,7 @@
         False,
         True,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "Une fibrose interstitielle diffuse idiopathique",

diff --git a/tests/pipelines/ner/disorders/cerebrovascular_accident.py b/tests/pipelines/ner/disorders/cerebrovascular_accident.py
@@ -8,7 +8,7 @@
         True,
         True,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "Patient hospitalisé à AVC.",

diff --git a/tests/pipelines/ner/disorders/congestive_heart_failure.py b/tests/pipelines/ner/disorders/congestive_heart_failure.py
@@ -6,7 +6,7 @@
         True,
         False,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "Présence d'un oedème pulmonaire",

diff --git a/tests/pipelines/ner/disorders/connective_tissue_disease.py b/tests/pipelines/ner/disorders/connective_tissue_disease.py
@@ -6,7 +6,7 @@
         True,
         True,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "Présence d'une sclérodermie.",

diff --git a/tests/pipelines/ner/disorders/dementia.py b/tests/pipelines/ner/disorders/dementia.py
@@ -5,7 +5,7 @@
         False,
         True,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "D'importants déficits cognitifs",

diff --git a/tests/pipelines/ner/disorders/hemiplegia.py b/tests/pipelines/ner/disorders/hemiplegia.py
@@ -4,7 +4,7 @@
         True,
         True,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "Patient hémiplégique",

diff --git a/tests/pipelines/ner/disorders/leukemia.py b/tests/pipelines/ner/disorders/leukemia.py
@@ -5,7 +5,7 @@
         True,
         True,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "Sydrome myéloprolifératif",

diff --git a/tests/pipelines/ner/disorders/lymphoma.py b/tests/pipelines/ner/disorders/lymphoma.py
@@ -5,7 +5,7 @@
         True,
         False,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "Un lymphome de Hodgkin.",

diff --git a/tests/pipelines/ner/disorders/myocardial_infarction.py b/tests/pipelines/ner/disorders/myocardial_infarction.py
@@ -6,7 +6,7 @@
         False,
         True,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "Une cardiopathie ischémique",

diff --git a/tests/pipelines/ner/disorders/peptic_ulcer_disease.py b/tests/pipelines/ner/disorders/peptic_ulcer_disease.py
@@ -5,7 +5,7 @@
         False,
         True,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "Beaucoup d'ulcères gastriques",

diff --git a/tests/pipelines/ner/disorders/peripheral_vascular_disease.py b/tests/pipelines/ner/disorders/peripheral_vascular_disease.py
@@ -14,7 +14,7 @@
         True,
         False,
     ],
-    detailled_status="PRESENT",
+    detailled_status=None,
     assign=None,
     texts=[
         "Un AOMI",

diff --git a/tests/pipelines/ner/disorders/test_all.py b/tests/pipelines/ner/disorders/test_all.py
@@ -72,7 +72,7 @@ def __init__(
             else len(texts) * [detailled_status]
         )
         self.assign = assign if assign is not None else len(texts) * [None]
-        self.negation = negation
+        self.negation = negation if negation is not None else len(texts) * [None]
 
         self.nlp.add_pipe(f"eds.{disorder}")
 
@@ -124,26 +124,3 @@ def test_disorder(normalized_nlp, disorder):
     )
 
     expect.check()
-
-
-def test_behavior_negation(blank_nlp):
-    blank_nlp.add_pipe("eds.normalizer")
-    blank_nlp.add_pipe("eds.tobacco")
-    blank_nlp.add_pipe("eds.alcohol")
-    blank_nlp.add_pipe("eds.negation")
-
-    negated_texts = [
-        "Le patient ne fume aucun truc.",
-        "Le patient fume 0 PA.",
-        "Il ne boit pas d'alcool." "Boit très rarement de l'alcool.",
-    ]
-
-    positive_texts = ["Le patient ne fume que le soir.", "Il ne boit plus d'alcool."]
-
-    for text in negated_texts:
-        doc = blank_nlp(text)
-        assert doc.ents[0]._.negation is True, text
-
-    for text in positive_texts:
-        doc = blank_nlp(text)
-        assert doc.ents[0]._.negation is False, text
diff --git a/tests/pipelines/ner/disorders/tobacco.py b/tests/pipelines/ner/disorders/tobacco.py
@@ -7,17 +7,32 @@
         True,
         True,
         True,
+        True,
+        True,
     ],
     detailled_status=[
-        "PRESENT",
-        "PRESENT",
+        None,
+        None,
         None,
         "ABSTINENCE",
-        "ABSENT",
-        "ABSENT",
+        None,
+        None,
         "ABSTINENCE",
+        None,
+        None,
+    ],
+    negation=[
+        None,
+        None,
+        None,
+        None,
+        True,
+        True,
+        None,
+        True,
+        True,
     ],
-    assign=[{"PA": 15}] + 6 * [None],
+    assign=[{"PA": 15}] + 8 * [None],
     texts=[
         "Tabagisme évalué à 15 PA",
         "Patient tabagique",
@@ -26,5 +41,7 @@
         "Tabac: 0",
         "Tabagisme passif",
         "Tabac: sevré depuis 5 ans",
+        "Le patient ne fume aucun truc.",
+        "Le patient fume 0 PA.",
     ],
 )