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), )