def test_add_sample_metadata():
for storage in get_storages():
storage.delete_all()
sm = SampleMetadata(storage=storage)
sample_name = "sample_name"
colour = sm.add_sample(sample_name)
assert sm.samples_to_colours([sample_name]) == {sample_name: 0}
assert sm.colours_to_samples([0]) == {0: sample_name}
assert sm.num_samples == 1
assert sm.sample_name_exists(sample_name)
assert not sm.sample_name_exists("sample_name2")
sample_name = "sample_name2"
colour = sm.add_sample(sample_name)
assert sm.sample_to_colour(sample_name) == 1
assert sm.colour_to_sample(1) == sample_name
assert sm.num_samples == 2
def migrate(mapping_filepath, storage_engine, storage_filename=None):
config = determine_config(storage_engine, storage_filename)
storage = get_storage(config)
current_metadata = SampleMetadata(storage)
with open(mapping_filepath, 'rb') as infile:
mapping = pickle.load(infile)
for old_id in mapping:
new_id = mapping.get(old_id)
if new_id and new_id != old_id:
colour = current_metadata.sample_to_colour(old_id)
if colour:
current_metadata._validate_sample_name(new_id)
current_metadata._set_sample_colour(new_id, colour)
current_metadata._set_colour_sample(colour, new_id)
current_metadata._set_sample_colour(old_id, -1)
storage.sync()
storage.close()