def test_write_json_with_info(self):
"""correctly writes an object with info attribute from json"""
# create a mock object that pretends like it's been derived from
# something
from cogent3.app.result import generic_result
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme")
obj = generic_result(source=join("blah", "delme.json"))
obj["dna"] = DNA
writer = io_app.write_json(outdir, create=True)
_ = writer(obj)
reader = io_app.load_json()
got = reader(join(outdir, "delme.json"))
got.deserialised_values()
self.assertEqual(got["dna"], DNA)
# now with a zipped archive
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme.zip")
obj = generic_result(source=join("blah", "delme.json"))
obj["dna"] = DNA
writer = io_app.write_json(outdir, create=True)
identifier = writer(obj)
reader = io_app.load_json()
got = reader(writer.data_store[0])
got.deserialised_values()
self.assertEqual(got["dna"], DNA)
expect = join(outdir.replace(".zip", ""), "delme.json")
if expect.startswith("." + os.sep):
expect = expect[2:]
self.assertEqual(identifier, expect)
def test_keys(self):
"""it works"""
data = {"type": "cogent3.core.moltype.MolType", "moltype": "dna"}
result = generic_result(source="blah.json")
result["key"] = data
keys = result.keys()
self.assertEqual(keys, ["key"])
def test_repr_str(self):
"""it works"""
data = {"type": "cogent3.core.moltype.MolType", "moltype": "dna"}
result = generic_result(source="blah.json")
result["key"] = data
r = repr(result)
s = str(result)
def test_roundtrip_tuple_key(self):
"""deserialise_result handles tuples as keys"""
from cogent3.app.result import generic_result
r = generic_result(source="none")
r[(1, 2)] = 24
got = deserialise_object(r.to_json())
self.assertEqual(got[(1, 2)], 24)
def test_deserialised_values(self):
"""correctly deserialises values"""
from cogent3 import DNA
data = {"type": "cogent3.core.moltype.MolType", "moltype": "dna"}
result = generic_result(source="blah.json")
result["key"] = data
result.deserialised_values()
got = result["key"]
self.assertEqual(got, DNA)
# if we have a type value without "cogent3", leaves as is
data = {"type": "core.moltype.MolType", "moltype": "dna"}
result = generic_result(source="blah.json")
result["key"] = data
result.deserialised_values()
got = result["key"]
self.assertEqual(got, data)
# or if no "type" entry, leaves as is
data = {"moltype": "dna"}
result = generic_result(source="blah.json")
result["key"] = data
result.deserialised_values()
got = result["key"]
self.assertEqual(got, data)
def test_write_json_with_info(self):
"""correctly writes an object with info attribute from json"""
# create a mock object that pretends like it's been derived from
# something
from cogent3.app.result import generic_result
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme")
obj = generic_result(source=join("blah", "delme.json"))
obj["dna"] = DNA
writer = io_app.write_json(outdir, create=True)
_ = writer(obj)
reader = io_app.load_json()
got = reader(join(outdir, "delme.json"))
got.deserialised_values()
self.assertEqual(got["dna"], DNA)
def _get_generic_result(source):
"""creates a generic result with a DNA moltype as the single value"""
gr = generic_result(source=source)
gr["dna"] = DNA
return gr
def test_invalid_setitem(self):
"""generic_result raise TypeError if trying to set invalid item type for json"""
gr = generic_result("null")
with self.assertRaises(TypeError):
gr["null"] = {0, 23}