Merge pull request #5264 from lfiedler/issue-5230

Fix ResourceWarnings during unittest

.github/contributors/lfiedler.md

@@ -0,0 +1,106 @@
+# spaCy contributor agreement
+
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+## Contributor Details
+
+| Field                          | Entry                |
+|------------------------------- | -------------------- |
+| Name                           | Leander Fiedler      |
+| Company name (if applicable)   |                      |
+| Title or role (if applicable)  |                      |
+| Date                           | 06 April 2020        |
+| GitHub username                | lfiedler             |
+| Website (optional)             |                      |

spacy/kb.pyx

@@ -445,10 +445,10 @@ cdef class KnowledgeBase:
 
 cdef class Writer:
     def __init__(self, object loc):
-        if path.exists(loc):
-            assert not path.isdir(loc), "%s is directory." % loc
         if isinstance(loc, Path):
             loc = bytes(loc)
+        if path.exists(loc):
+            assert not path.isdir(loc), "%s is directory." % loc
         cdef bytes bytes_loc = loc.encode('utf8') if type(loc) == unicode else loc
         self._fp = fopen(<char*>bytes_loc, 'wb')
         if not self._fp:
@@ -490,10 +490,10 @@ cdef class Writer:
 
 cdef class Reader:
     def __init__(self, object loc):
-        assert path.exists(loc)
-        assert not path.isdir(loc)
         if isinstance(loc, Path):
             loc = bytes(loc)
+        assert path.exists(loc)
+        assert not path.isdir(loc)
         cdef bytes bytes_loc = loc.encode('utf8') if type(loc) == unicode else loc
         self._fp = fopen(<char*>bytes_loc, 'rb')
         if not self._fp:

spacy/language.py

@@ -907,9 +907,8 @@ class Language(object):
         serializers["tokenizer"] = lambda p: self.tokenizer.to_disk(
             p, exclude=["vocab"]
         )
-        serializers["meta.json"] = lambda p: p.open("w").write(
-            srsly.json_dumps(self.meta)
-        )
+        serializers["meta.json"] = lambda p: srsly.write_json(p, self.meta)
+
         for name, proc in self.pipeline:
             if not hasattr(proc, "name"):
                 continue

spacy/pipeline/pipes.pyx

@@ -203,7 +203,7 @@ class Pipe(object):
         serialize["cfg"] = lambda p: srsly.write_json(p, self.cfg)
         serialize["vocab"] = lambda p: self.vocab.to_disk(p)
         if self.model not in (None, True, False):
-            serialize["model"] = lambda p: p.open("wb").write(self.model.to_bytes())
+            serialize["model"] = lambda p: self.model.to_disk(p)
         exclude = util.get_serialization_exclude(serialize, exclude, kwargs)
         util.to_disk(path, serialize, exclude)
 
@@ -626,7 +626,7 @@ class Tagger(Pipe):
         serialize = OrderedDict((
             ("vocab", lambda p: self.vocab.to_disk(p)),
             ("tag_map", lambda p: srsly.write_msgpack(p, tag_map)),
-            ("model", lambda p: p.open("wb").write(self.model.to_bytes())),
+            ("model", lambda p: self.model.to_disk(p)),
             ("cfg", lambda p: srsly.write_json(p, self.cfg))
         ))
         exclude = util.get_serialization_exclude(serialize, exclude, kwargs)
@@ -1395,7 +1395,7 @@ class EntityLinker(Pipe):
         serialize["vocab"] = lambda p: self.vocab.to_disk(p)
         serialize["kb"] = lambda p: self.kb.dump(p)
         if self.model not in (None, True, False):
-            serialize["model"] = lambda p: p.open("wb").write(self.model.to_bytes())
+            serialize["model"] = lambda p: self.model.to_disk(p)
         exclude = util.get_serialization_exclude(serialize, exclude, kwargs)
         util.to_disk(path, serialize, exclude)
 

spacy/tests/regression/test_issue5230.py

@@ -0,0 +1,142 @@
+# coding: utf8
+import warnings
+from unittest import TestCase
+
+import pytest
+import srsly
+from numpy import zeros
+from spacy.kb import KnowledgeBase, Writer
+from spacy.vectors import Vectors
+
+from spacy.language import Language
+from spacy.pipeline import Pipe
+from spacy.tests.util import make_tempdir
+
+
+def nlp():
+    return Language()
+
+
+def vectors():
+    data = zeros((3, 1), dtype="f")
+    keys = ["cat", "dog", "rat"]
+    return Vectors(data=data, keys=keys)
+
+
+def custom_pipe():
+    # create dummy pipe partially implementing interface -- only want to test to_disk
+    class SerializableDummy(object):
+        def __init__(self, **cfg):
+            if cfg:
+                self.cfg = cfg
+            else:
+                self.cfg = None
+            super(SerializableDummy, self).__init__()
+
+        def to_bytes(self, exclude=tuple(), disable=None, **kwargs):
+            return srsly.msgpack_dumps({"dummy": srsly.json_dumps(None)})
+
+        def from_bytes(self, bytes_data, exclude):
+            return self
+
+        def to_disk(self, path, exclude=tuple(), **kwargs):
+            pass
+
+        def from_disk(self, path, exclude=tuple(), **kwargs):
+            return self
+
+    class MyPipe(Pipe):
+        def __init__(self, vocab, model=True, **cfg):
+            if cfg:
+                self.cfg = cfg
+            else:
+                self.cfg = None
+            self.model = SerializableDummy()
+            self.vocab = SerializableDummy()
+
+    return MyPipe(None)
+
+
+def tagger():
+    nlp = Language()
+    nlp.add_pipe(nlp.create_pipe("tagger"))
+    tagger = nlp.get_pipe("tagger")
+    # need to add model for two reasons:
+    # 1. no model leads to error in serialization,
+    # 2. the affected line is the one for model serialization
+    tagger.begin_training(pipeline=nlp.pipeline)
+    return tagger
+
+
+def entity_linker():
+    nlp = Language()
+    nlp.add_pipe(nlp.create_pipe("entity_linker"))
+    entity_linker = nlp.get_pipe("entity_linker")
+    # need to add model for two reasons:
+    # 1. no model leads to error in serialization,
+    # 2. the affected line is the one for model serialization
+    kb = KnowledgeBase(nlp.vocab, entity_vector_length=1)
+    entity_linker.set_kb(kb)
+    entity_linker.begin_training(pipeline=nlp.pipeline)
+    return entity_linker
+
+
+objects_to_test = (
+    [nlp(), vectors(), custom_pipe(), tagger(), entity_linker()],
+    ["nlp", "vectors", "custom_pipe", "tagger", "entity_linker"],
+)
+
+
+def write_obj_and_catch_warnings(obj):
+    with make_tempdir() as d:
+        with warnings.catch_warnings(record=True) as warnings_list:
+            warnings.filterwarnings("always", category=ResourceWarning)
+            obj.to_disk(d)
+            # in python3.5 it seems that deprecation warnings are not filtered by filterwarnings
+            return list(filter(lambda x: isinstance(x, ResourceWarning), warnings_list))
+
+
+@pytest.mark.parametrize("obj", objects_to_test[0], ids=objects_to_test[1])
+def test_to_disk_resource_warning(obj):
+    warnings_list = write_obj_and_catch_warnings(obj)
+    assert len(warnings_list) == 0
+
+
+def test_writer_with_path_py35():
+    writer = None
+    with make_tempdir() as d:
+        path = d / "test"
+        try:
+            writer = Writer(path)
+        except Exception as e:
+            pytest.fail(str(e))
+        finally:
+            if writer:
+                writer.close()
+
+
+def test_save_and_load_knowledge_base():
+    nlp = Language()
+    kb = KnowledgeBase(nlp.vocab, entity_vector_length=1)
+    with make_tempdir() as d:
+        path = d / "kb"
+        try:
+            kb.dump(path)
+        except Exception as e:
+            pytest.fail(str(e))
+
+        try:
+            kb_loaded = KnowledgeBase(nlp.vocab, entity_vector_length=1)
+            kb_loaded.load_bulk(path)
+        except Exception as e:
+            pytest.fail(str(e))
+
+
+class TestToDiskResourceWarningUnittest(TestCase):
+    def test_resource_warning(self):
+        scenarios = zip(*objects_to_test)
+
+        for scenario in scenarios:
+            with self.subTest(msg=scenario[1]):
+                warnings_list = write_obj_and_catch_warnings(scenario[0])
+                self.assertEqual(len(warnings_list), 0)

spacy/vectors.pyx

@@ -383,8 +383,16 @@ cdef class Vectors:
             save_array = lambda arr, file_: xp.save(file_, arr, allow_pickle=False)
         else:
             save_array = lambda arr, file_: xp.save(file_, arr)
+
+        def save_vectors(path):
+            # the source of numpy.save indicates that the file object is closed after use.
+            # but it seems that somehow this does not happen, as ResourceWarnings are raised here.
+            # in order to not rely on this, wrap in context manager.
+            with path.open("wb") as _file:
+                save_array(self.data, _file)
+
         serializers = OrderedDict((
-            ("vectors", lambda p: save_array(self.data, p.open("wb"))),
+            ("vectors", lambda p: save_vectors(p)),
             ("key2row", lambda p: srsly.write_msgpack(p, self.key2row))
         ))
         return util.to_disk(path, serializers, [])