def save_metadata(item, collection, cache=None, sidecar_on_failure=True):
'''
save the writable key values in item.meta to the image (translating picty native keys
in the `meta` attribute of item to IPTC/XMP/Exif standard keys as necessary)
'''
fname = collection.get_path(item)
if 'sidecar' in item.__dict__:
if os.path.exists(collection.get_path(item.sidecar)):
result = metadata.save_sidecar(item,
collection.get_path(item.sidecar))
else:
del item.sidecar
result = metadata.save_metadata(item, fname)
else:
result = metadata.save_metadata(item, fname)
if result:
item.mtime = io.get_mtime(
fname
) ##todo: this and the next line should be a method of the image class
update_thumb_date(item, collection, cache)
return True
else:
if sidecar_on_failure and 'sidecar' not in item.__dict__:
item.sidecar = item.uid + '.xmp'
metadata.create_sidecar(item, collection.get_path(item),
collection.get_path(item.sidecar))
return metadata.save_sidecar(item,
collection.get_path(item.sidecar))
return False
def got_torrent(self):
binhash, address, data, dtype, start_time = self.metadata_queue.get()
if dtype == 'pt':
self.n_downloading_pt -= 1
elif dtype == 'lt':
self.n_downloading_lt -= 1
if not data:
return
self.n_valid += 1
save_metadata(self.dbcurr, binhash, address, start_time, data)
self.n_new += 1
def got_torrent(self):
binhash, address, data, dtype, start_time = self.metadata_queue.get()
if dtype == 'pt':
self.n_downloading_pt -= 1
elif dtype == 'lt':
self.n_downloading_lt -= 1
if not data:
return
self.n_valid += 1
save_metadata(self.dbcurr, binhash, address, start_time, data)
self.n_new += 1
def run(self):
while True:
try:
infohash, address, info, start_time = self.q.get()
md.save_metadata(self.cursor, infohash, address, start_time,
info)
except Exception, e:
traceback.print_stack()
logging.error("error occured while DBWriter running : " +
str(e))
def setup_h5_dataset(
bin_file,
ref_fasta,
chromsizes,
h5_file,
label_sets,
signal_sets,
bin_size,
stride,
final_length,
reverse_complemented,
onehot_features_key,
tmp_dir,
binned=True):
"""given a region file, set up dataset
conventionally, this is 1 chromosome
"""
# make sure tmp dir exists
os.system("mkdir -p {}".format(tmp_dir))
# set up prefix
prefix = os.path.basename(bin_file).split(
".narrrowPeak")[0].split(".bed")[0]
# save in the metadata
save_metadata(bin_file, h5_file)
# generate BED annotations on the active center
for key in label_sets.keys():
label_files = label_sets[key][0]
label_params = label_sets[key][1]
method = label_params.get("method", "half_peak")
generate_labels(
bin_file, label_files, key, h5_file,
method=method, chromsizes=chromsizes,
tmp_dir=tmp_dir)
return h5_file
def save_metadata(item,collection,cache=None,sidecar_on_failure=True):
'''
save the writable key values in item.meta to the image (translating picty native keys
in the `meta` attribute of item to IPTC/XMP/Exif standard keys as necessary)
'''
fname=collection.get_path(item)
if 'sidecar' in item.__dict__:
if os.path.exists(collection.get_path(item.sidecar)):
result = metadata.save_sidecar(item,collection.get_path(item.sidecar))
else:
del item.sidecar
result = metadata.save_metadata(item,fname)
else:
result = metadata.save_metadata(item,fname)
if result:
item.mtime=io.get_mtime(fname) ##todo: this and the next line should be a method of the image class
update_thumb_date(item,collection,cache)
return True
else:
if sidecar_on_failure and 'sidecar' not in item.__dict__:
item.sidecar=item.uid + '.xmp'
metadata.create_sidecar(item,collection.get_path(item),collection.get_path(item.sidecar))
return metadata.save_sidecar(item,collection.get_path(item.sidecar))
return False
