biluo_tags_from_offsets throw exception for overlapping entities (#4021)

* Check whether two entities overlap

- biluo_gold_biluo_overlap now throw exception when entities passed in have overlaps
- added unit test

* SCA agreement

.github/contributors/ryanzhe.md

@@ -0,0 +1,106 @@
+# spaCy contributor agreement
+
+This spaCy Contributor Agreement (**"SCA"**) is based on the
+[Oracle Contributor Agreement](http://www.oracle.com/technetwork/oca-405177.pdf).
+The SCA applies to any contribution that you make to any product or project
+managed by us (the **"project"**), and sets out the intellectual property rights
+you grant to us in the contributed materials. The term **"us"** shall mean
+[ExplosionAI UG (haftungsbeschränkt)](https://explosion.ai/legal). The term
+**"you"** shall mean the person or entity identified below.
+
+If you agree to be bound by these terms, fill in the information requested
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+folder [`.github/contributors/`](/.github/contributors/). The name of the file
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+
+Read this agreement carefully before signing. These terms and conditions
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+
+## Contributor Agreement
+
+1. The term "contribution" or "contributed materials" means any source code,
+object code, patch, tool, sample, graphic, specification, manual,
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+
+2. With respect to any worldwide copyrights, or copyright applications and
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+
+    * you hereby assign to us joint ownership, and to the extent that such
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+
+    * you agree that each of us can do all things in relation to your
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+    * at our option, to sublicense these same rights to third parties through
+    multiple levels of sublicensees or other licensing arrangements.
+
+4. Except as set out above, you keep all right, title, and interest in your
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+
+5. You covenant, represent, warrant and agree that:
+
+    * Each contribution that you submit is and shall be an original work of
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+    * each contribution shall be in compliance with U.S. export control laws and
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+    participation in the project, including the fact that you have signed the SCA.
+
+6. This SCA is governed by the laws of the State of California and applicable
+U.S. Federal law. Any choice of law rules will not apply.
+
+7. Please place an “x” on one of the applicable statement below. Please do NOT
+mark both statements:
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+    * [ ] I am signing on behalf of myself as an individual and no other person
+    or entity, including my employer, has or will have rights with respect my
+    contributions.
+
+    * [x] I am signing on behalf of my employer or a legal entity and I have the
+    actual authority to contractually bind that entity.
+
+## Contributor Details
+
+| Field                          | Entry                |
+|------------------------------- | -------------------- |
+| Name                           | Ziming He            |
+| Company name (if applicable)   | Georgia Tech         |
+| Title or role (if applicable)  | Student              |
+| Date                           | 2019-07-24           |
+| GitHub username                | RyanZHe              |
+| Website (optional)             | www.papermachine.me  |

spacy/gold.pyx

@@ -678,11 +678,23 @@ def biluo_tags_from_offsets(doc, entities, missing="O"):
         >>> tags = biluo_tags_from_offsets(doc, entities)
         >>> assert tags == ["O", "O", 'U-LOC', "O"]
     """
+    # Ensure no overlapping entity labels exist
+    tokens_in_ents = {}
+       
     starts = {token.idx: token.i for token in doc}
     ends = {token.idx + len(token): token.i for token in doc}
     biluo = ["-" for _ in doc]
     # Handle entity cases
     for start_char, end_char, label in entities:
+        for token_index in range(start_char, end_char):
+            if token_index in tokens_in_ents.keys():
+                raise ValueError(Errors.E103.format(
+                    span1=(tokens_in_ents[token_index][0],
+                            tokens_in_ents[token_index][1],
+                            tokens_in_ents[token_index][2]),
+                    span2=(start_char, end_char, label)))
+            tokens_in_ents[token_index] = (start_char, end_char, label)
+
         start_token = starts.get(start_char)
         end_token = ends.get(end_char)
         # Only interested if the tokenization is correct

spacy/tests/test_gold.py

@@ -4,7 +4,7 @@ from __future__ import unicode_literals
 from spacy.gold import biluo_tags_from_offsets, offsets_from_biluo_tags
 from spacy.gold import spans_from_biluo_tags, GoldParse
 from spacy.tokens import Doc
-
+import pytest
 
 def test_gold_biluo_U(en_vocab):
     words = ["I", "flew", "to", "London", "."]
@@ -32,6 +32,14 @@ def test_gold_biluo_BIL(en_vocab):
     tags = biluo_tags_from_offsets(doc, entities)
     assert tags == ["O", "O", "O", "B-LOC", "I-LOC", "L-LOC", "O"]
 
+def test_gold_biluo_overlap(en_vocab):
+    words = ["I", "flew", "to", "San", "Francisco", "Valley", "."]
+    spaces = [True, True, True, True, True, False, True]
+    doc = Doc(en_vocab, words=words, spaces=spaces)
+    entities = [(len("I flew to "), len("I flew to San Francisco Valley"), "LOC"),
+    (len("I flew to "), len("I flew to San Francisco"), "LOC")]
+    with pytest.raises(ValueError):
+        tags = biluo_tags_from_offsets(doc, entities)
 
 def test_gold_biluo_misalign(en_vocab):
     words = ["I", "flew", "to", "San", "Francisco", "Valley."]