fix: allow deep attributes in Standoff and OMOP doc2dict converters

Author: percevalw

changelog.md

@@ -14,6 +14,7 @@
 
 - Support packaging with poetry 2.0
 - Solve pickling issues with multiprocessing when pytorch is installed
+- Allow deep attributes like `a.b.c` for `span_attributes` in Standoff and OMOP doc2dict converters
 
 # v0.15.0 (2024-12-13)
 

edsnlp/data/converters.py

@@ -355,6 +355,14 @@ def __init__(
 
     def __call__(self, doc):
         spans = get_spans(doc, self.span_getter)
+        span_binding_getters = {
+            obj_name: BINDING_GETTERS[
+                ("_." + ext_name)
+                if ext_name.split(".")[0] not in SPAN_BUILTIN_ATTRS
+                else ext_name
+            ]
+            for ext_name, obj_name in self.span_attributes.items()
+        }
         obj = {
             FILENAME: doc._.note_id,
             "doc_id": doc._.note_id,
@@ -369,9 +377,12 @@ def __call__(self, doc):
                         }
                     ],
                     "attributes": {
-                        obj_name: getattr(ent._, ext_name)
-                        for ext_name, obj_name in self.span_attributes.items()
-                        if ent._.has(ext_name)
+                        obj_name: value
+                        for obj_name, value in (
+                            (k, getter(ent))
+                            for k, getter in span_binding_getters.items()
+                        )
+                        if value is not None
                     },
                     "label": ent.label_,
                 }
@@ -621,8 +632,11 @@ def __call__(self, doc):
                     "lexical_variant": ent.text,
                     "note_nlp_source_value": ent.label_,
                     **{
-                        obj_name: getter(ent)
-                        for obj_name, getter in span_binding_getters.items()
+                        obj_name: value
+                        for obj_name, value in (
+                            (k, getter(ent))
+                            for k, getter in span_binding_getters.items()
+                        )
                     },
                 }
                 for i, ent in enumerate(sorted(dict.fromkeys(spans)))

edsnlp/utils/bindings.py

@@ -19,9 +19,14 @@ def _check_path(path: str):
         "The label must be a path of valid python identifier to be used as a getter"
         "in the following template: span.[YOUR_LABEL], such as `label_` or `_.negated"
     )
-    if path[0].isalpha() or path[0] == "_":
-        return "." + path
-    return path
+    parts = path.split(".")
+    new_path = "span"
+    for part in parts:
+        if " " in part:
+            new_path = "getattr(" + new_path + f", {part!r})"
+        elif len(part) > 0:
+            new_path += "." + part
+    return new_path
 
 
 def make_binding_getter(attribute: Union[str, Binding]):
@@ -47,7 +52,7 @@ def make_binding_getter(attribute: Union[str, Binding]):
         exec(
             f"def getter(span):\n"
             f"    try:\n"
-            f"        return span{path} == value\n"
+            f"        return {path} == value\n"
             f"    except AttributeError:\n"
             f"        return False\n",
             ctx,
@@ -60,7 +65,7 @@ def make_binding_getter(attribute: Union[str, Binding]):
         exec(
             f"def getter(span):\n"
             f"    try:\n"
-            f"        return span{path}\n"
+            f"        return {path}\n"
             f"    except AttributeError:\n"
             f"        return None\n",
             ctx,
@@ -88,12 +93,12 @@ def make_binding_setter(binding: Binding):
     if isinstance(binding, tuple):
         path, value = binding
         path = _check_path(path)
-        fn_string = f"""def setter(span): span{path} = value"""
+        fn_string = f"""def setter(span): {path} = value"""
         ctx = {"value": value}
         exec(fn_string, ctx, ctx)
     else:
         path = _check_path(binding)
-        fn_string = f"""def setter(span, value): span{path} = value"""
+        fn_string = f"""def setter(span, value): {path} = value"""
         ctx = {}
         exec(fn_string, ctx, ctx)
     return ctx["setter"]