def _update_path_to_data(self, d_list):
if not isinstance(d_list, list):
d_list = [d_list]
for d in d_list:
if not d.path_to_data or any([len(x) > 255 for x in d.path_to_data.split("/")]):
logger.debug("Updating 'path_to_data' from '{}'...".format(d.path_to_data))
d.path_to_data = elaspic_database.get_uniprot_base_path(d) + elaspic_database.get_uniprot_domain_path(d)
logger.debug("to '{}'...".format(d.path_to_data))
self.db.merge_row(d)
os.makedirs(op.join(conf.CONFIGS["archive_temp_dir"], d.path_to_data), exist_ok=True)
def _update_path_to_data(self, d_list):
if not isinstance(d_list, list):
d_list = [d_list]
for d in d_list:
if not d.path_to_data or any(
[len(x) > 255 for x in d.path_to_data.split("/")]):
logger.debug("Updating 'path_to_data' from '{}'...".format(
d.path_to_data))
d.path_to_data = elaspic_database.get_uniprot_base_path(
d) + elaspic_database.get_uniprot_domain_path(d)
logger.debug("to '{}'...".format(d.path_to_data))
self.db.merge_row(d)
os.makedirs(op.join(conf.CONFIGS["archive_temp_dir"],
d.path_to_data),
exist_ok=True)
def __exit__(self, exc_type, exc_value, traceback):
d = self.d
if exc_type is not None:
return False
if self.provean_supset_file is None:
provean = elaspic_database_tables.Provean()
provean.uniprot_id = d.uniprot_id
provean.provean_supset_filename = op.basename(self.sequence.provean_supset_file)
provean.provean_supset_length = self.sequence.provean_supset_length
self.db.merge_provean(
provean,
self.sequence.provean_supset_file,
conf.CONFIGS["copy_data"] and elaspic_database.get_uniprot_base_path(d),
)
def __init__(self, d, db):
self.d = d
self.db = db
self.sequence = None
self.skip = False
if d.uniprot_sequence and d.uniprot_sequence.provean and d.uniprot_sequence.provean.provean_supset_filename:
# Provean supset has already been calculated
self.provean_supset_file = op.join(
conf.CONFIGS["archive_temp_dir"],
elaspic_database.get_uniprot_base_path(d),
d.uniprot_sequence.provean.provean_supset_filename,
)
else:
self.provean_supset_file = None
def __init__(self, d, db):
self.d = d
self.db = db
self.sequence = None
self.skip = False
if (d.uniprot_sequence and d.uniprot_sequence.provean
and d.uniprot_sequence.provean.provean_supset_filename):
# Provean supset has already been calculated
self.provean_supset_file = op.join(
conf.CONFIGS["archive_temp_dir"],
elaspic_database.get_uniprot_base_path(d),
d.uniprot_sequence.provean.provean_supset_filename,
)
else:
self.provean_supset_file = None
def __exit__(self, exc_type, exc_value, traceback):
d = self.d
if exc_type is not None:
return False
if self.provean_supset_file is None:
provean = elaspic_database_tables.Provean()
provean.uniprot_id = d.uniprot_id
provean.provean_supset_filename = op.basename(
self.sequence.provean_supset_file)
provean.provean_supset_length = self.sequence.provean_supset_length
self.db.merge_provean(
provean,
self.sequence.provean_supset_file,
conf.CONFIGS["copy_data"]
and elaspic_database.get_uniprot_base_path(d),
)
