def test_unchanged_database_record(self):
"""tests unchanged record via the Readable and Writable DataStore interface to TinyDB"""
from cogent3.app.io import load_db
from copy import deepcopy
loader = load_db()
data = self.data
original_record = deepcopy(data)
with TemporaryDirectory(dir=".") as dirname:
path = os.path.join(dirname, self.basedir)
dstore = self.WriteClass(path, if_exists="overwrite")
id_ = dstore.make_relative_identifier(list(data).pop(0))
m = dstore.write(id_, data)
data.pop(set(data.keys()).pop())
got = loader(m)
self.assertNotEqual(got, data)
self.assertEqual(got, original_record)
data = deepcopy(original_record)
m = dstore.write(id_, data)
data[set(data.keys()).pop()] = None
got = loader(m)
self.assertNotEqual(got, data)
self.assertEqual(got, original_record)
data = deepcopy(original_record)
m = dstore.write(id_, data)
data.clear()
got = loader(m)
self.assertNotEqual(got, data)
self.assertEqual(got, original_record)
dstore.close()
def test_bootstrap_composability(self):
"""can be composed with load_db and write_db"""
m1 = evo_app.model("F81")
m2 = evo_app.model("HKY85")
hyp = evo_app.hypothesis(m1, m2)
with TemporaryDirectory(dir=".") as dirname:
path = join(dirname, "delme.tinydb")
_ = io.load_db() + evo_app.bootstrap(
hyp, num_reps=2) + io.write_db(path)
def test_write_db_load_db2(self):
"""correctly write/load built-in python from tinydb"""
with TemporaryDirectory(dir=".") as dirname:
outpath = join(dirname, "delme")
writer = write_db(outpath, create=True, if_exists="ignore")
data = dict(a=[1, 2], b="string")
m = writer(data, identifier=join("blah", "delme.json"))
writer.data_store.db.close()
dstore = io_app.get_data_store(f"{outpath}.tinydb", suffix="json")
reader = io_app.load_db()
got = reader(dstore[0])
dstore.close()
self.assertEqual(got, data)
def test_write_db_load_db(self):
"""correctly write/load from tinydb"""
# straight directory
with TemporaryDirectory(dir=".") as dirname:
outpath = join(dirname, "delme")
writer = write_db(outpath, create=True, if_exists="ignore")
gr = _get_generic_result(join("blah", "delme.json"))
got = writer(gr)
writer.data_store.db.close()
dstore = io_app.get_data_store(f"{outpath}.tinydb", suffix="json")
reader = io_app.load_db()
got = reader(dstore[0])
dstore.close()
got.deserialised_values()
self.assertIsInstance(got["dna"], DNA.__class__)
self.assertEqual(got["dna"], DNA)
def test_write_db_load_db(self):
"""correctly write/load from tinydb"""
# straight directory
with TemporaryDirectory(dir=".") as dirname:
outpath = join(dirname, "delme")
writer = write_db(outpath, create=True, if_exists="ignore")
mock = patch("data.source", autospec=True)
mock.to_json = DNA.to_json
mock.source = join("blah", "delme.json")
got = writer(mock)
writer.data_store.db.close()
dstore = io_app.get_data_store(f"{outpath}.tinydb", suffix="json")
reader = io_app.load_db()
got = reader(dstore[0])
dstore.close()
self.assertIsInstance(got, DNA.__class__)
self.assertEqual(got, DNA)
def test_load_db_failure_json_file(self):
"""informative load_db error message when given a json file path"""
# todo this test has a trapped exception about being unable to delete
# a file
with TemporaryDirectory(dir=".") as dirname:
outpath = join(dirname, "delme")
writer = write_db(outpath, create=True, if_exists="ignore")
gr = _get_generic_result(join("blah", "delme.json"))
got = writer(gr)
writer.data_store.db.close()
dstore = io_app.get_data_store(f"{outpath}.tinydb", suffix="json")
reader = io_app.load_db()
outpath = join(dirname, "dummy.json")
with open(outpath, mode="w") as outfile:
outfile.write("\n\n")
got = reader(outpath)
self.assertIsInstance(got, NotCompleted)
self.assertTrue("json" in got.message)
