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if recipe_name == 'fasta' and genome in rgc.genomes_list() \
and 'fasta' in rgc.list_assets_by_genome(genome):
_LOGGER.warning("'{g}' genome is already initialized with other fasta asset ({g}/{a}:{t}). "
"It will be re-initialized.".format(g=genome, a=asset_key, t=asset_tag))
if not build_asset(genome, asset_key, asset_tag, asset_build_package, genome_outfolder,
specified_args, specified_params, **input_assets):
log_path = os.path.abspath(os.path.join(genome_outfolder, asset_key, asset_tag,
BUILD_STATS_DIR, ORI_LOG_NAME))
_LOGGER.info("'{}/{}:{}' was not added to the config, but directory has been left in place. "
"See the log file for details: {}".format(genome, asset_key, asset_tag, log_path))
return
# If the recipe was a fasta, we init the genome
if recipe_name == 'fasta':
_LOGGER.info("Computing initial genome digest...")
collection_checksum, content_checksums = \
fasta_checksum(_seek(rgc, genome, asset_key, asset_tag, "fasta"))
_LOGGER.info("Initializing genome...")
refgenie_initg(rgc, genome, content_checksums)
_LOGGER.info("Finished building '{}' asset".format(asset_key))
with rgc as r:
# update asset relationships
r.update_relatives_assets(genome, asset_key, asset_tag, parent_assets) # adds parents
for i in parent_assets:
parsed_parent = parse_registry_path(i)
# adds child (currently built asset) to the parent
r.update_relatives_assets(parsed_parent["genome"], parsed_parent["asset"], parsed_parent["tag"],
["{}/{}:{}".format(genome, asset_key, asset_tag)], True)
if args.genome_description is not None:
_LOGGER.debug("adding genome ({}) description: '{}'".format(genome, args.genome_description))
r.update_genomes(genome, {CFG_GENOME_DESC_KEY: args.genome_description})
if args.tag_description is not None:
_LOGGER.debug("adding tag ({}/{}:{}) description: '{}'".format(genome, asset_key, asset_tag,