def convert_metadata(infile, config):
in_metadata = db.DB()
in_metadata.set_cachesize(4, 0)
in_metadata.open(infile + "/metadata", flags=db.DB_RDONLY)
bloom_filter_size = int.from_bytes(in_metadata[b'bloom_filter_size'],
'big')
kmer_size = int.from_bytes(in_metadata[b'kmer_size'], 'big')
num_hashes = int.from_bytes(in_metadata[b'num_hashes'], 'big')
colours = pickle.loads(in_metadata[b'colours'])
num_samples = len(colours)
## Create the sample metadata
colour_sample = {}
for colour in range(num_samples):
key = "colour%i" % colour
key = key.encode("utf-8")
sample_name = in_metadata[key].decode('utf-8')
colour_sample[colour] = sample_name
## Add the sample metadata
storage = get_storage(config)
sm = SampleMetadata(storage)
for colour, sample_name in colour_sample.items():
if "DELETE" in sample_name:
sample_name = "D3L3T3D"
print(colour, sample_name)
sm._set_colour_sample(colour, sample_name)
sm._set_sample_colour(sample_name, -1)
else:
sm._set_sample_colour(sample_name, colour)
sm._set_colour_sample(colour, sample_name)
sm._set_integer(sm.colour_count_key, num_samples)
in_metadata.close()
return num_samples
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()