def test_write_json_no_info(self):
"""correctly writes an object with out an info attribute from json"""
# create a mock object that pretends like it's been derived from
# something
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme")
mock = patch("data.source", autospec=True)
mock.to_rich_dict = DNA.to_rich_dict
mock.source = join("blah", "delme.json")
writer = io_app.write_json(outdir, create=True)
_ = writer(mock)
reader = io_app.load_json()
got = reader(writer.data_store[0])
self.assertEqual(got, DNA)
# now with a zipped archive
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme.zip")
mock = patch("data.source", autospec=True)
mock.to_rich_dict = DNA.to_rich_dict
mock.source = join("blah", "delme.json")
writer = io_app.write_json(outdir, create=True)
identifier = writer(mock)
reader = io_app.load_json()
# checking loadable from a data store member too
got = reader(writer.data_store[0])
self.assertEqual(got, DNA)
expect = join(outdir.replace(".zip", ""), "delme.json")
if expect.startswith("." + os.sep):
expect = expect[2:]
self.assertEqual(identifier, expect)
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_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.util.union_dict import UnionDict
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme")
mock = Mock()
mock.to_rich_dict = DNA.to_rich_dict
mock.info = UnionDict(source=join("blah", "delme.json"))
writer = io_app.write_json(outdir, create=True)
_ = writer(mock)
reader = io_app.load_json()
got = reader(join(outdir, "delme.json"))
self.assertEqual(got, DNA)
# now with a zipped archive
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme.zip")
mock = Mock()
mock.to_rich_dict = DNA.to_rich_dict
mock.info = UnionDict(source=join("blah", "delme.json"))
writer = io_app.write_json(outdir, create=True)
identifier = writer(mock)
reader = io_app.load_json()
got = reader(writer.data_store[0])
self.assertEqual(got, DNA)
expect = join(outdir.replace(".zip", ""), "delme.json")
if expect.startswith("." + os.sep):
expect = expect[2:]
self.assertEqual(identifier, expect)
def _get_all_composables(tmp_dir_name):
test_model1 = evo.model("HKY85")
test_model2 = evo.model("GN")
test_hyp = evo.hypothesis(test_model1, test_model2)
test_num_reps = 100
applications = [
align.align_to_ref(),
align.progressive_align(model="GY94"),
evo.ancestral_states(),
evo.bootstrap(hyp=test_hyp, num_reps=test_num_reps),
evo.hypothesis(test_model1, test_model2),
evo.model("GN"),
evo.tabulate_stats(),
sample.fixed_length(100),
sample.min_length(100),
io.write_db(tmp_dir_name, create=True),
io.write_json(tmp_dir_name, create=True),
io.write_seqs(tmp_dir_name, create=True),
sample.omit_bad_seqs(),
sample.omit_degenerates(),
sample.omit_duplicated(),
sample.take_codon_positions(1),
sample.take_named_seqs(),
sample.trim_stop_codons(gc=1),
translate.select_translatable(),
tree.quick_tree(),
tree.scale_branches(),
tree.uniformize_tree(),
]
return applications
def test_write_json_no_info(self):
"""correctly writes an object with out an info attribute from json"""
# create a mock object that pretends like it's been derived from
# something
with TemporaryDirectory(dir=".") as dirname:
outdir = join(dirname, "delme")
gr = _get_generic_result(join("blah", "delme.json"))
writer = io_app.write_json(outdir, create=True)
_ = writer(gr)
reader = io_app.load_json()
got = reader(writer.data_store[0])
got.deserialised_values()
self.assertEqual(got["dna"], DNA)
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)
