💫 Fix interaction of lemmatizer and tokenizer exceptions (#3388)

Closes #2203. Closes #3268.

Lemmas set from outside the `Morphology` class were being overwritten. The result was especially confusing when deserialising, as it meant some lemmas could change when storing and retrieving a `Doc` object.

This PR applies two fixes:

1) When we go to set the lemma in the `Morphology` class, first check whether a lemma is already set. If so, don't overwrite.
2) When we load with `doc.from_array()`, take care to apply the `TAG` field first. This allows other fields to overwrite the `TAG` implied properties, if they're provided explicitly (e.g. the `LEMMA`).

## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.

spacy/morphology.pyx

@@ -110,7 +110,8 @@ cdef class Morphology:
             analysis.lemma = self.lemmatize(analysis.tag.pos, token.lex.orth,
                                             self.tag_map.get(tag_str, {}))
             self._cache.set(tag_id, token.lex.orth, analysis)
-        token.lemma = analysis.lemma
+        if token.lemma == 0:
+            token.lemma = analysis.lemma
         token.pos = analysis.tag.pos
         token.tag = analysis.tag.name
         token.morph = analysis.tag.morph

spacy/tests/regression/test_issue2001-2500.py

@@ -2,6 +2,7 @@
 from __future__ import unicode_literals
 
 import pytest
+import numpy
 from spacy.tokens import Doc
 from spacy.displacy import render
 from spacy.gold import iob_to_biluo
@@ -39,6 +40,26 @@ def test_issue2179():
     assert nlp2.get_pipe("ner").labels == ("CITIZENSHIP",)
 
 
+def test_issue2203(en_vocab):
+    """Test that lemmas are set correctly in doc.from_array."""
+    words = ["I", "'ll", "survive"]
+    tags = ["PRP", "MD", "VB"]
+    lemmas = ["-PRON-", "will", "survive"]
+    tag_ids = [en_vocab.strings.add(tag) for tag in tags]
+    lemma_ids = [en_vocab.strings.add(lemma) for lemma in lemmas]
+    doc = Doc(en_vocab, words=words)
+    # Work around lemma corrpution problem and set lemmas after tags
+    doc.from_array("TAG", numpy.array(tag_ids, dtype="uint64"))
+    doc.from_array("LEMMA", numpy.array(lemma_ids, dtype="uint64"))
+    assert [t.tag_ for t in doc] == tags
+    assert [t.lemma_ for t in doc] == lemmas
+    # We need to serialize both tag and lemma, since this is what causes the bug
+    doc_array = doc.to_array(["TAG", "LEMMA"])
+    new_doc = Doc(doc.vocab, words=words).from_array(["TAG", "LEMMA"], doc_array)
+    assert [t.tag_ for t in new_doc] == tags
+    assert [t.lemma_ for t in new_doc] == lemmas
+
+
 def test_issue2219(en_vocab):
     vectors = [("a", [1, 2, 3]), ("letter", [4, 5, 6])]
     add_vecs_to_vocab(en_vocab, vectors)

spacy/tokens/doc.pyx

@@ -763,17 +763,18 @@ cdef class Doc:
             attr_ids[i] = attr_id
         if len(array.shape) == 1:
             array = array.reshape((array.size, 1))
+        # Do TAG first. This lets subsequent loop override stuff like POS, LEMMA
+        if TAG in attrs:
+            col = attrs.index(TAG)
+            for i in range(length):
+                if array[i, col] != 0:
+                    self.vocab.morphology.assign_tag(&tokens[i], array[i, col])
         # Now load the data
         for i in range(self.length):
             token = &self.c[i]
             for j in range(n_attrs):
-                Token.set_struct_attr(token, attr_ids[j], array[i, j])
+                if attr_ids[j] != TAG:
-        # Auxiliary loading logic
+                    Token.set_struct_attr(token, attr_ids[j], array[i, j])
-        for col, attr_id in enumerate(attrs):
-            if attr_id == TAG:
-                for i in range(length):
-                    if array[i, col] != 0:
-                        self.vocab.morphology.assign_tag(&tokens[i], array[i, col])
         # Set flags
         self.is_parsed = bool(self.is_parsed or HEAD in attrs or DEP in attrs)
         self.is_tagged = bool(self.is_tagged or TAG in attrs or POS in attrs)