raise error when setting overlapping entities as doc.ents to close #2550

spacy/errors.py

@@ -250,7 +250,9 @@ class Errors(object):
     E096 = ("Invalid object passed to displaCy: Can only visualize Doc or "
              "Span objects, or dicts if set to manual=True.")
     E097 = ("Can't merge non-disjoint spans. '{token}' is already part of tokens to merge")
-
+    E098 = ("Trying to set conflicting doc.ents: '{span1}' and '{span2}'. A token"
+            " can only be part of one entity, so make sure the entities you're "
+            "setting don't overlap.")
 
 @add_codes
 class TempErrors(object):

spacy/tests/doc/test_add_entities.py

@@ -3,6 +3,7 @@
 
 from ...pipeline import EntityRecognizer
 from ..util import get_doc
+from ...tokens import Span
 
 import pytest
 
@@ -22,3 +23,13 @@ def test_doc_add_entities_set_ents_iob(en_vocab):
 
     doc.ents = [(doc.vocab.strings['WORD'], 0, 2)]
     assert [w.ent_iob_ for w in doc] == ['B', 'I', '', '']
+
+def test_add_overlapping_entities(en_vocab):
+    text = ["Louisiana", "Office", "of", "Conservation"]
+    doc = get_doc(en_vocab, text)
+    entity = Span(doc, 0, 4, label=391)
+    doc.ents = [entity]
+
+    new_entity = Span(doc, 0, 1, label=392)
+    with pytest.raises(ValueError):
+        doc.ents = list(doc.ents) + [new_entity]

spacy/tests/regression/test_issue242.py

@@ -17,9 +17,10 @@ def test_issue242(en_tokenizer):
     matcher.add('FOOD', None, *patterns)
 
     matches = [(ent_type, start, end) for ent_type, start, end in matcher(doc)]
-    doc.ents += tuple(matches)
     match1, match2 = matches
     assert match1[1] == 3
     assert match1[2] == 5
     assert match2[1] == 4
     assert match2[2] == 6
+
+    doc.ents += tuple([match2])

spacy/tokens/doc.pyx

@@ -458,22 +458,29 @@ cdef class Doc:
             #    prediction
             # 3. Test basic data-driven ORTH gazetteer
             # 4. Test more nuanced date and currency regex
+
+            tokens_in_ents = {}
+            cdef attr_t entity_type
+            cdef int ent_start, ent_end
+            for ent_info in ents:
+                entity_type, ent_start, ent_end = get_entity_info(ent_info)
+                for token_index in range(ent_start, ent_end):
+                    if token_index in tokens_in_ents.keys():
+                        raise ValueError(Errors.E098.format(
+                            span1=(tokens_in_ents[token_index][0],
+                                   tokens_in_ents[token_index][1],
+                                   self.vocab.strings[tokens_in_ents[token_index][2]]),
+                            span2=(ent_start, ent_end, self.vocab.strings[entity_type])))
+                    tokens_in_ents[token_index] = (ent_start, ent_end, entity_type)
+
             cdef int i
             for i in range(self.length):
                 self.c[i].ent_type = 0
                 self.c[i].ent_iob = 0  # Means missing.
             cdef attr_t ent_type
             cdef int start, end
             for ent_info in ents:
-                if isinstance(ent_info, Span):
-                    ent_id = ent_info.ent_id
-                    ent_type = ent_info.label
-                    start = ent_info.start
-                    end = ent_info.end
-                elif len(ent_info) == 3:
-                    ent_type, start, end = ent_info
-                else:
-                    ent_id, ent_type, start, end = ent_info
+                ent_type, start, end = get_entity_info(ent_info)
                 if ent_type is None or ent_type < 0:
                     # Mark as O
                     for i in range(start, end):
@@ -1062,3 +1069,14 @@ def fix_attributes(doc, attributes):
             attributes[ENT_TYPE] = doc.vocab.strings[attributes['label']]
     if 'ent_type' in attributes:
         attributes[ENT_TYPE] = attributes['ent_type']
+
+def get_entity_info(ent_info):
+    if isinstance(ent_info, Span):
+        ent_type = ent_info.label
+        start = ent_info.start
+        end = ent_info.end
+    elif len(ent_info) == 3:
+        ent_type, start, end = ent_info
+    else:
+        ent_id, ent_type, start, end = ent_info
+    return ent_type, start, end