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import io
from collections import OrderedDict, namedtuple
from typing import NamedTuple
import numpy as np
import pytest
import yaml
import asdf
from asdf import tagged, treeutil, yamlutil
from asdf.compat.numpycompat import NUMPY_LT_1_14
from asdf.exceptions import AsdfWarning
from . import helpers
def test_ordered_dict(tmp_path):
"""
Test that we can write out and read in ordered dicts.
"""
tree = {
"ordered_dict": OrderedDict([("first", "foo"), ("second", "bar"), ("third", "baz")]),
"unordered_dict": {"first": "foo", "second": "bar", "third": "baz"},
}
def check_asdf(asdf):
tree = asdf.tree
assert isinstance(tree["ordered_dict"], OrderedDict)
assert list(tree["ordered_dict"].keys()) == ["first", "second", "third"]
assert not isinstance(tree["unordered_dict"], OrderedDict)
assert isinstance(tree["unordered_dict"], dict)
def check_raw_yaml(content):
assert b"OrderedDict" not in content
helpers.assert_roundtrip_tree(tree, tmp_path, asdf_check_func=check_asdf, raw_yaml_check_func=check_raw_yaml)
def test_unicode_write(tmp_path):
"""
We want to write unicode out as regular utf-8-encoded
characters, not as escape sequences
"""
tree = {"ɐʇɐp‾ǝpoɔıun": 42, "ascii_only": "this is ascii"}
def check_asdf(asdf):
assert "ɐʇɐp‾ǝpoɔıun" in asdf.tree
assert isinstance(asdf.tree["ascii_only"], str)
def check_raw_yaml(content):
# Ensure that unicode is written out as UTF-8 without escape
# sequences
assert "ɐʇɐp‾ǝpoɔıun".encode() in content
# Ensure that the unicode "tag" is not used
assert b"unicode" not in content
helpers.assert_roundtrip_tree(tree, tmp_path, asdf_check_func=check_asdf, raw_yaml_check_func=check_raw_yaml)
def test_arbitrary_python_object():
"""
Putting "just any old" Python object in the tree should raise an
exception.
"""
class Foo:
pass
tree = {"object": Foo()}
buff = io.BytesIO()
ff = asdf.AsdfFile(tree)
with pytest.raises(yaml.YAMLError):
ff.write_to(buff)
def run_tuple_test(tree, tmp_path):
def check_asdf(asdf):
assert isinstance(asdf.tree["val"], list)
def check_raw_yaml(content):
assert b"tuple" not in content
# Ignore these warnings for the tests that don't actually test the warning
init_options = dict(ignore_implicit_conversion=True)
helpers.assert_roundtrip_tree(
tree, tmp_path, asdf_check_func=check_asdf, raw_yaml_check_func=check_raw_yaml, init_options=init_options
)
def test_python_tuple(tmp_path):
"""
We don't want to store tuples as tuples, because that's not a
built-in YAML data type. This test ensures that they are
converted to lists.
"""
tree = {"val": (1, 2, 3)}
run_tuple_test(tree, tmp_path)
def test_named_tuple_collections(tmp_path):
"""
Ensure that we are able to serialize a collections.namedtuple.
"""
nt = namedtuple("TestNamedTuple1", ("one", "two", "three"))
tree = {"val": nt(1, 2, 3)}
run_tuple_test(tree, tmp_path)
def test_named_tuple_typing(tmp_path):
"""
Ensure that we are able to serialize a typing.NamedTuple.
"""
nt = NamedTuple("TestNamedTuple2", (("one", int), ("two", int), ("three", int)))
tree = {"val": nt(1, 2, 3)}
run_tuple_test(tree, tmp_path)
def test_named_tuple_collections_recursive(tmp_path):
nt = namedtuple("TestNamedTuple3", ("one", "two", "three"))
tree = {"val": nt(1, 2, np.ones(3))}
def check_asdf(asdf):
assert (asdf.tree["val"][2] == np.ones(3)).all()
init_options = dict(ignore_implicit_conversion=True)
helpers.assert_roundtrip_tree(tree, tmp_path, asdf_check_func=check_asdf, init_options=init_options)
def test_named_tuple_typing_recursive(tmp_path):
nt = NamedTuple("TestNamedTuple4", (("one", int), ("two", int), ("three", np.ndarray)))
tree = {"val": nt(1, 2, np.ones(3))}
def check_asdf(asdf):
assert (asdf.tree["val"][2] == np.ones(3)).all()
init_options = dict(ignore_implicit_conversion=True)
helpers.assert_roundtrip_tree(tree, tmp_path, asdf_check_func=check_asdf, init_options=init_options)
def test_implicit_conversion_warning():
nt = namedtuple("TestTupleWarning", ("one", "two", "three"))
tree = {"val": nt(1, 2, np.ones(3))}
with pytest.warns(AsdfWarning, match=r"Failed to serialize instance"):
with asdf.AsdfFile(tree):
pass
with helpers.assert_no_warnings():
with asdf.AsdfFile(tree, ignore_implicit_conversion=True):
pass
@pytest.mark.xfail(reason="pyyaml has a bug and does not support tuple keys")
def test_python_tuple_key(tmp_path):
"""
This tests whether tuple keys are round-tripped properly.
As of this writing, this does not work in pyyaml but does work in
ruamel.yaml. If/when we decide to switch to ruamel.yaml, this test should
pass.
"""
tree = {(42, 1): "foo"}
helpers.assert_roundtrip_tree(tree, tmp_path)
def test_tags_removed_after_load(tmp_path):
tree = {"foo": ["bar", (1, 2, None)]}
def check_asdf(asdf):
for node in treeutil.iter_tree(asdf.tree):
if node != asdf.tree:
assert not isinstance(node, tagged.Tagged)
helpers.assert_roundtrip_tree(tree, tmp_path, asdf_check_func=check_asdf)
def test_explicit_tags():
yaml = """#ASDF {}
%YAML 1.1
--- !<tag:stsci.edu:asdf/core/asdf-1.0.0>
foo: !<tag:stsci.edu:asdf/core/ndarray-1.0.0> [1, 2, 3]
...
""".format(
asdf.versioning.default_version
)
# Check that fully qualified explicit tags work
buff = helpers.yaml_to_asdf(yaml, yaml_headers=False)
with asdf.open(buff) as ff:
assert all(ff.tree["foo"] == [1, 2, 3])
def test_yaml_internal_reference(tmp_path):
"""
Test that YAML internal references (anchors and aliases) work,
as well as recursive data structures.
"""
d = {
"foo": "2",
}
d["bar"] = d
_list = []
_list.append(_list)
tree = {"first": d, "second": d, "list": _list}
def check_yaml(content):
assert b"list:&id002-*id002" in b"".join(content.split())
helpers.assert_roundtrip_tree(tree, tmp_path, raw_yaml_check_func=check_yaml)
def test_yaml_nan_inf():
tree = {"a": np.nan, "b": np.inf, "c": -np.inf}
buff = io.BytesIO()
ff = asdf.AsdfFile(tree)
ff.write_to(buff)
buff.seek(0)
with asdf.open(buff) as ff:
assert np.isnan(ff.tree["a"])
assert np.isinf(ff.tree["b"])
assert np.isinf(ff.tree["c"])
def test_tag_object():
class SomeObject:
pass
tag = "tag:nowhere.org:none/some/thing"
instance = tagged.tag_object(tag, SomeObject())
assert instance._tag == tag
@pytest.mark.parametrize(
"numpy_value,expected_value",
[
(np.str_("foo"), "foo"),
(np.bytes_("foo"), b"foo"),
(np.float16(3.14), 3.14),
(np.float32(3.14159), 3.14159),
(np.float64(3.14159), 3.14159),
# Evidently float128 is not available on Windows:
(getattr(np, "float128", np.float64)(3.14159), 3.14159),
(np.int8(42), 42),
(np.int16(42), 42),
(np.int32(42), 42),
(np.int64(42), 42),
(np.longlong(42), 42),
(np.uint8(42), 42),
(np.uint16(42), 42),
(np.uint32(42), 42),
(np.uint64(42), 42),
(np.ulonglong(42), 42),
],
)
def test_numpy_scalar(numpy_value, expected_value):
ctx = asdf.AsdfFile({"value": numpy_value})
tree = ctx.tree
buffer = io.BytesIO()
yamlutil.dump_tree(tree, buffer, ctx)
buffer.seek(0)
if isinstance(expected_value, float) and NUMPY_LT_1_14:
assert yamlutil.load_tree(buffer)["value"] == pytest.approx(expected_value, rel=0.001)
else:
assert yamlutil.load_tree(buffer)["value"] == expected_value
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