diff --git a/bio_parser/parse/nested_document.py b/bio_parser/parse/nested_document.py
index 664d65d961631c2d1b06576c7a0ba3f17951f199..e4a2e08cdfb020eeafde4e8ddd57c535477d8640 100644
--- a/bio_parser/parse/nested_document.py
+++ b/bio_parser/parse/nested_document.py
@@ -208,16 +208,48 @@ class NestedDocument:
nested_tokens: list[NestedToken] = field(default_factory=list)
"""List of the nested tokens in the Document"""
- spans: list[Span] = field(default_factory=list)
- """List of the spans in the Document"""
-
nested_spans: list[NestedSpan] = field(default_factory=list)
"""List of the nested spans in the Document"""
hierarchy: list[dict[str, Any]] = field(default_factory=list)
"""Hierarchy required for metrics"""
+ def __post_init__(self):
+ """Parses the tokens and the entity spans in the document."""
+ # Build nested spans with hierarchy
+ self.nested_spans = self._build_nested_spans()
+
+ # Build JSON hierarchy
+ self.hierarchy = self._build_hierarchy()
+
+ def _build_nested_spans(self) -> list[dict[str, Span | list[Span]]]:
+ """Build span hierarchy based on token position in the BIO file."""
+
+ def is_inside(span, parent_span):
+ return (
+ (span.idx >= parent_span.idx)
+ and (span.end <= parent_span.end)
+ and (parent_span != span)
+ )
+
+ flat_spans = self._build_spans()
+ nested_spans = []
+ parents = [span for span in flat_spans if span.level == 0]
+ for parent in parents:
+ children = [
+ span
+ for span in flat_spans
+ if is_inside(span, parent) and parent.level < span.level
+ ]
+ nested_spans.append(NestedSpan([parent] + children))
+ return nested_spans
+
+ def _build_hierarchy(self) -> list[dict]:
+ return [nested_span.hierarchy for nested_span in self.nested_spans]
+
def _build_spans(self):
+ """Build spans."""
+ spans = []
current_spans: dict[str, Span] = {} # Keep track of current spans by category
for idx, line in enumerate(self.bio_repr.splitlines()):
try:
@@ -230,7 +262,7 @@ class NestedDocument:
case Tag.OUTSIDE:
# Close all current spans
for span in current_spans.values():
- self.spans.append(span)
+ spans.append(span)
current_spans = {}
case Tag.INSIDE:
@@ -244,7 +276,7 @@ class NestedDocument:
# End existing span if necessary
if token.label in current_spans:
span = current_spans.pop(token.label)
- self.spans.append(span)
+ spans.append(span)
# Start a new span
current_spans[token.label] = Span()
@@ -256,42 +288,8 @@ class NestedDocument:
# Last spans
for span in current_spans.values():
- self.spans.append(span)
-
- def _build_nested_spans(self) -> list[dict[str, Span | list[Span]]]:
- """Build span hierarchy based on token position in the BIO file."""
-
- def is_inside(span, parent_span):
- return (
- (span.idx >= parent_span.idx)
- and (span.end <= parent_span.end)
- and (parent_span != span)
- )
-
- self.nested_spans = []
- parents = [span for span in self.spans if span.level == 0]
- for parent in parents:
- children = [
- span
- for span in self.spans
- if is_inside(span, parent) and parent.level < span.level
- ]
- self.nested_spans.append(NestedSpan([parent] + children))
-
- def _build_hierarchy(self) -> list[dict]:
- self.hierarchy = [nested_span.hierarchy for nested_span in self.nested_spans]
- return self.hierarchy
-
- def __post_init__(self):
- """Parses the tokens and the entity spans in the document."""
- # Build spans
- self._build_spans()
-
- # Build nested spans with hierarchy
- self._build_nested_spans()
-
- # Build a simple hierarchy
- self._build_hierarchy()
+ spans.append(span)
+ return spans
@property
def words(self) -> list[str]:
@@ -302,7 +300,17 @@ class NestedDocument:
def entities(self) -> list[tuple[str, str]]:
"""List of entities making up the document."""
return list(
- map(attrgetter("label", "text"), filter(attrgetter("label"), self.spans)),
+ map(
+ attrgetter("label", "text"),
+ filter(
+ attrgetter("label"),
+ [
+ span
+ for nested_span in self.nested_spans
+ for span in nested_span.spans
+ ],
+ ),
+ ),
)
@property
diff --git a/bio_parser/parse/validate.py b/bio_parser/parse/validate.py
index ca097852ab6a5f3cdc0791531c45086b273d8fe4..ebf26b6709ec404ac6aad20d5c6a26783a6334e1 100644
--- a/bio_parser/parse/validate.py
+++ b/bio_parser/parse/validate.py
@@ -25,7 +25,7 @@ def run(filepaths: list[Path], allow_nested=False) -> None:
else Document.from_file(filepath)
)
filepath.with_suffix(".json").write_text(json.dumps(asdict(doc), indent=2))
+ logger.info(f"The file @ `{filepath}` is valid!")
except Exception as e:
logger.error(f"Could not load the file @ `{filepath}`: {e}")
- logger.info(f"The file @ `{filepath}` is valid!")
diff --git a/tests/parse/test_validate.py b/tests/parse/test_validate.py
index 646d0ef398b23eef73bc6eae7e0eb5b1daf05e2b..56fda91a35986a5b8427d2366efb65f84fc1c79e 100644
--- a/tests/parse/test_validate.py
+++ b/tests/parse/test_validate.py
@@ -71,42 +71,6 @@ def test_valid_nested():
{"idx": 13, "text": "mère O"},
{"idx": 14, "text": "Marie B-mother B-name"},
],
- "spans": [
- {
- "tokens": [
- {"idx": 0, "text": "Charles B-child", "level": 0},
- {"idx": 1, "text": "né I-child", "level": 0},
- {"idx": 2, "text": "Ã I-child", "level": 0},
- {"idx": 3, "text": "Beaune I-child", "level": 0},
- {"idx": 4, "text": "en I-child", "level": 0},
- {"idx": 5, "text": "1836 I-child", "level": 0},
- ]
- },
- {"tokens": [{"idx": 0, "text": "Charles B-name", "level": 1}]},
- {"tokens": [{"idx": 3, "text": "Beaune B-location", "level": 1}]},
- {"tokens": [{"idx": 5, "text": "1836 B-date", "level": 1}]},
- {
- "tokens": [
- {"idx": 7, "text": "Jean B-father", "level": 0},
- {"idx": 8, "text": "Bigre I-father", "level": 0},
- {"idx": 9, "text": "charpentier I-father", "level": 0},
- {"idx": 10, "text": "de I-father", "level": 0},
- {"idx": 11, "text": "cette I-father", "level": 0},
- {"idx": 12, "text": "paroisse I-father", "level": 0},
- ]
- },
- {"tokens": [{"idx": 7, "text": "Jean B-name", "level": 1}]},
- {"tokens": [{"idx": 8, "text": "Bigre B-surname", "level": 1}]},
- {"tokens": [{"idx": 9, "text": "charpentier B-occupation", "level": 1}]},
- {
- "tokens": [
- {"idx": 11, "text": "cette B-location", "level": 1},
- {"idx": 12, "text": "paroisse I-location", "level": 1},
- ]
- },
- {"tokens": [{"idx": 14, "text": "Marie B-mother", "level": 0}]},
- {"tokens": [{"idx": 14, "text": "Marie B-name", "level": 1}]},
- ],
"nested_spans": [
{
"spans": [