def test_load_unaligned_seqs_from_json(self):
"""test loading an unaligned object from json file"""
with TemporaryDirectory(dir=".") as dirname:
json_path = os.path.join(dirname, "unaligned.json")
path = os.path.join(data_path, "brca1_5.paml")
unaligned = load_unaligned_seqs(path)
unaligned.write(json_path)
got = load_unaligned_seqs(json_path)
self.assertIsInstance(got, SequenceCollection)
self.assertEqual(got.to_dict(), unaligned.to_dict())
self.assertEqual(got.info["source"], path)
# tests json generated by make_record_for_json
uncompleted_record = make_record_for_json("delme", got, False)
uncompleted_record_path = os.path.join(dirname,
"uncompleted_record.json")
completed_record = make_record_for_json("delme", got, True)
completed_record_path = os.path.join(dirname,
"completed_record.json")
with open(uncompleted_record_path, "w") as out:
out.write(json.dumps(uncompleted_record))
with open(completed_record_path, "w") as out:
out.write(json.dumps(completed_record))
# tests when provided record json file is uncompleted
with self.assertRaises(TypeError):
load_unaligned_seqs(uncompleted_record_path)
# tests when provided record json is completed
got = load_unaligned_seqs(completed_record_path)
self.assertIsInstance(got, SequenceCollection)
self.assertEqual(got.to_dict(), unaligned.to_dict())
self.assertEqual(got.info["source"], path)
def test_load_aligned_seqs_from_json(self):
"""tests loading an aligned object from json file"""
with TemporaryDirectory(dir=".") as dirname:
path = os.path.join(data_path, "brca1_5.paml")
alignment = load_aligned_seqs(path,
array_align=False,
moltype="dna")
alignment_json_path = os.path.join(dirname, "alignment.json")
alignment.write(alignment_json_path)
array_alignment = load_aligned_seqs(path, moltype="dna")
array_alignment_json_path = os.path.join(dirname,
"array_alignment.json")
array_alignment.write(array_alignment_json_path)
# tests case Alignment
got = load_aligned_seqs(alignment_json_path)
self.assertIsInstance(got, Alignment)
self.assertEqual(got.moltype.label, "dna")
self.assertEqual(got.to_dict(), alignment.to_dict())
self.assertEqual(got.info["source"], path)
# tests case ArrayAlignment
got = load_aligned_seqs(array_alignment_json_path)
self.assertIsInstance(got, ArrayAlignment)
self.assertEqual(got.moltype.label, "dna")
self.assertEqual(got.to_dict(), array_alignment.to_dict())
self.assertEqual(got.info["source"], path)
# tests json generated by make_record_for_json
uncompleted_record = make_record_for_json("delme", got, False)
completed_record = make_record_for_json("delme", got, True)
uncompleted_record_path = os.path.join(dirname,
"uncompleted_record.json")
completed_record_path = os.path.join(dirname,
"completed_record.json")
with open(uncompleted_record_path, "w") as out:
out.write(json.dumps(uncompleted_record))
with open(completed_record_path, "w") as out:
out.write(json.dumps(completed_record))
# tests when provided record json file is uncompleted
with self.assertRaises(TypeError):
load_unaligned_seqs(uncompleted_record_path)
# tests when provided record json is completed
got = load_aligned_seqs(completed_record_path)
self.assertIsInstance(got, ArrayAlignment)
self.assertEqual(got.to_dict(), array_alignment.to_dict())
self.assertEqual(got.info["source"], path)
# tests wrong input json file
json_path = os.path.join(dirname, "unaligned.json")
path = os.path.join(data_path, "brca1_5.paml")
unaligned = load_unaligned_seqs(path)
unaligned.write(json_path)
with self.assertRaises(TypeError):
load_aligned_seqs(json_path)
def test_load_json(self):
"""correctly loads an object from json"""
from cogent3.app.data_store import make_record_for_json
data = make_record_for_json("delme", DNA, True)
data = json.dumps(data)
# straight directory
with TemporaryDirectory(dir=".") as dirname:
outpath = join(dirname, "delme.json")
with open(outpath, "w") as outfile:
outfile.write(data)
reader = io_app.load_json()
got = reader(outpath)
self.assertIsInstance(got, DNA.__class__)
self.assertEqual(got, DNA)
# zipped directory
with TemporaryDirectory(dir=".") as dirname:
zip_path = join(dirname, "delme.zip")
outpath = "delme/delme.json"
with zipfile.ZipFile(zip_path, "a") as out:
out.writestr(outpath, data)
dstore = io_app.get_data_store(zip_path, suffix="json")
member = dstore.get_member("delme.json")
reader = io_app.load_json()
got = reader(member)
self.assertIsInstance(got, DNA.__class__)
self.assertEqual(got, DNA)
