def refgenie_build(gencfg, genome, asset_list, recipe_name, args): """ Runs the refgenie build recipe. :param str gencfg: path to the genome configuration file :param argparse.Namespace args: parsed command-line options/arguments """ rgc = RefGenConf( filepath=gencfg, writable=False, skip_read_lock=_skip_lock(args.skip_read_lock, gencfg), ) specified_args = _parse_user_build_input(args.files) specified_params = _parse_user_build_input(args.params) def _read_json_file(filepath): """ Read a JSON file :param str filepath: path to the file to read :return dict: read data """ with open(filepath, "r") as f: data = json.load(f) return data if recipe_name and os.path.isfile(recipe_name) and recipe_name.endswith( ".json"): recipe_name = _read_json_file(filepath=recipe_name) if not hasattr(args, "outfolder") or not args.outfolder: # Default to genome_folder _LOGGER.debug("No outfolder provided, using genome config.") args.outfolder = rgc.data_dir def _build_asset( genome, asset_key, tag, build_pkg, genome_outfolder, specific_args, specific_params, alias, **kwargs, ): """ Builds assets with pypiper and updates a genome config file. This function actually run the build commands in a given build package, and then update the refgenie config file. :param str genome: The assembly key; e.g. 'mm10'. :param str asset_key: The unique asset identifier; e.g. 'bowtie2_index' :param dict build_pkg: A dict (see examples) specifying lists of required input_assets, commands to run, and outputs to register as assets. """ log_outfolder = os.path.abspath( os.path.join(genome_outfolder, asset_key, tag, BUILD_STATS_DIR)) _LOGGER.info("Saving outputs to:\n- content: {}\n- logs: {}".format( genome_outfolder, log_outfolder)) if args.docker: # Set up some docker stuff if args.volumes: # TODO: is volumes list defined here? volumes = volumes.append(genome_outfolder) else: volumes = genome_outfolder if not _writeable(genome_outfolder): _LOGGER.error( "Insufficient permissions to write to output folder: {}". format(genome_outfolder)) return pm = pypiper.PipelineManager(name="refgenie", outfolder=log_outfolder, args=args) tk = pypiper.NGSTk(pm=pm) if args.docker: pm.get_container(build_pkg[CONT], volumes) _LOGGER.debug("Asset build package: " + str(build_pkg)) # create a bundle list to simplify calls below gat = [genome, asset_key, tag] # collect variables required to populate the command templates asset_vars = get_asset_vars( genome, asset_key, tag, genome_outfolder, specific_args, specific_params, **kwargs, ) # populate command templates # prior to populating, remove any seek_key parts from the keys, since these are not supported by format method command_list_populated = [ x.format(**{k.split(".")[0]: v for k, v in asset_vars.items()}) for x in build_pkg[CMD_LST] ] # create output directory tk.make_dir(asset_vars["asset_outfolder"]) target = os.path.join(log_outfolder, TEMPLATE_TARGET.format(genome, asset_key, tag)) # add target command command_list_populated.append("touch {target}".format(target=target)) _LOGGER.debug("Command populated: '{}'".format( " ".join(command_list_populated))) try: # run build command signal.signal(signal.SIGINT, _handle_sigint(gat)) pm.run(command_list_populated, target, container=pm.container) except pypiper.exceptions.SubprocessError: _LOGGER.error("asset '{}' build failed".format(asset_key)) return False else: # save build recipe to the JSON-formatted file recipe_file_name = TEMPLATE_RECIPE_JSON.format(asset_key, tag) with open(os.path.join(log_outfolder, recipe_file_name), "w") as outfile: json.dump(build_pkg, outfile) # since the assets are always built to a standard dir structure, we # can just stitch a path together for asset digest calculation asset_dir = os.path.join(rgc.data_dir, *gat) if not os.path.exists(asset_dir): raise OSError("Could not compute asset digest. Path does not " "exist: {}".format(asset_dir)) digest = get_dir_digest(asset_dir) _LOGGER.info("Asset digest: {}".format(digest)) # add updates to config file with rgc as r: if asset_key == "fasta": r.update_genomes(genome, data={CFG_ALIASES_KEY: [alias]}, force_digest=genome) r.update_assets( *gat[0:2], data={CFG_ASSET_DESC_KEY: build_pkg[DESC]}, force_digest=genome, ) r.update_tags( *gat, force_digest=genome, data={ CFG_ASSET_PATH_KEY: asset_key, CFG_ASSET_CHECKSUM_KEY: digest, }, ) r.update_seek_keys( *gat, force_digest=genome, keys={ k: v.format(**asset_vars) for k, v in build_pkg[ASSETS].items() }, ) r.set_default_pointer(*gat, force_digest=genome) pm.stop_pipeline() return True for a in asset_list: asset_key = a["asset"] asset_tag = a["tag"] or rgc.get_default_tag( genome, a["asset"], use_existing=False) recipe_name = recipe_name or asset_key if isinstance( recipe_name, dict) or (isinstance(recipe_name, str) and recipe_name in asset_build_packages.keys()): if isinstance(recipe_name, dict): _LOGGER.info("Using custom recipe: \n{}".format(recipe_name)) asset_build_package = _check_recipe(recipe_name) recipe_name = asset_build_package["name"] else: asset_build_package = _check_recipe( asset_build_packages[recipe_name]) # handle user-requested parents for the required assets input_assets = {} parent_assets = [] specified_asset_keys, specified_assets = None, None if args.assets is not None: parsed_parents_input = _parse_user_build_input(args.assets) specified_asset_keys = list(parsed_parents_input.keys()) specified_assets = list(parsed_parents_input.values()) _LOGGER.debug(f"Custom assets requested: {args.assets}") if not specified_asset_keys and isinstance(args.assets, list): _LOGGER.warning( "Specified parent assets format is invalid. Using defaults." ) for req_asset in asset_build_package[REQ_ASSETS]: req_asset_data = parse_registry_path(req_asset[KEY]) # for each req asset see if non-default parents were requested if (specified_asset_keys is not None and req_asset_data["asset"] in specified_asset_keys): parent_data = parse_registry_path( specified_assets[specified_asset_keys.index( req_asset_data["asset"])]) g, a, t, s = ( parent_data["genome"], parent_data["asset"], parent_data["tag"] or rgc.get_default_tag(genome, parent_data["asset"]), parent_data["seek_key"], ) else: # if no custom parents requested for the req asset, use default one default = parse_registry_path(req_asset[DEFAULT]) g, a, t, s = ( genome, default["asset"], rgc.get_default_tag(genome, default["asset"]), req_asset_data["seek_key"], ) parent_assets.append("{}/{}:{}".format( rgc.get_genome_alias_digest(g, fallback=True), a, t)) input_assets[req_asset[KEY]] = _seek(rgc, g, a, t, s) _LOGGER.debug("Using parents: {}".format(", ".join(parent_assets))) _LOGGER.debug("Provided files: {}".format(specified_args)) _LOGGER.debug("Provided parameters: {}".format(specified_params)) for required_file in asset_build_package[REQ_FILES]: if (specified_args is None or required_file[KEY] not in specified_args.keys()): raise ValueError( "Path to the '{x}' input ({desc}) is required, but not provided. " "Specify it with: --files {x}=/path/to/{x}_file". format(x=required_file[KEY], desc=required_file[DESC])) for required_param in asset_build_package[REQ_PARAMS]: if specified_params is None: specified_params = {} if required_param[KEY] not in specified_params.keys(): if required_param[DEFAULT] is None: raise ValueError( "Value for the parameter '{x}' ({desc}) is required, but not provided. " "Specify it with: --params {x}=value".format( x=required_param[KEY], desc=required_param[DESC])) else: specified_params.update( {required_param[KEY]: required_param[DEFAULT]}) _LOGGER.info("Building '{}/{}:{}' using '{}' recipe".format( genome, asset_key, asset_tag, recipe_name)) ori_genome = genome if recipe_name == "fasta": if (genome in rgc.genomes_list() and "fasta" in rgc.list_assets_by_genome(genome)): pretag = rgc.get_default_tag(genome, "fasta") _LOGGER.warning( "'{g}' genome is already initialized with other fasta asset ({g}/{a}:{t})" .format(g=genome, a=asset_key, t=pretag)) genome = rgc.get_genome_alias_digest(alias=genome, fallback=True) else: # if the recipe is "fasta" we first initialiaze the genome, based on the provided path to the input FASTA file genome, _ = rgc.initialize_genome( fasta_path=specified_args["fasta"], alias=ori_genome, skip_alias_write=True, ) else: try: genome = rgc.get_genome_alias_digest(genome, fallback=True) except UndefinedAliasError: _LOGGER.error("Genome '{}' has not been initialized yet; " "no key found for this alias".format(genome)) return recipe_name = None genome_outfolder = os.path.join(args.outfolder, genome) if not _build_asset( genome, asset_key, asset_tag, asset_build_package, genome_outfolder, specified_args, specified_params, ori_genome, **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 _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, args.tag_description)) r.update_tags( genome, asset_key, asset_tag, {CFG_TAG_DESC_KEY: args.tag_description}, ) rgc._symlink_alias(genome, asset_key, asset_tag) else: _raise_missing_recipe_error(recipe_name)
def refgenie_build(gencfg, genome, asset_list, recipe_name, args): """ Runs the refgenie build recipe. :param str gencfg: path to the genome configuration file :param argparse.Namespace args: parsed command-line options/arguments """ rgc = RefGenConf(filepath=gencfg, writable=False) specified_args = _parse_user_build_input(args.files) specified_params = _parse_user_build_input(args.params) if not hasattr(args, "outfolder") or not args.outfolder: # Default to genome_folder _LOGGER.debug("No outfolder provided, using genome config.") args.outfolder = rgc[CFG_FOLDER_KEY] _LOGGER.debug("Default config file: {}".format(default_config_file())) if args.config_file and not os.path.isfile(args.config_file): _LOGGER.debug("Config file path isn't a file: {}".format( args.config_file)) args.config_file = default_config_file() def build_asset(genome, asset_key, tag, build_pkg, genome_outfolder, specific_args, specific_params, **kwargs): """ Builds assets with pypiper and updates a genome config file. This function actually run the build commands in a given build package, and then update the refgenie config file. :param str genome: The assembly key; e.g. 'mm10'. :param str asset_key: The unique asset identifier; e.g. 'bowtie2_index' :param dict build_pkg: A dict (see examples) specifying lists of required input_assets, commands to run, and outputs to register as assets. """ log_outfolder = os.path.abspath( os.path.join(genome_outfolder, asset_key, tag, BUILD_STATS_DIR)) _LOGGER.info("Saving outputs to:\n- content: {}\n- logs: {}".format( genome_outfolder, log_outfolder)) if args.docker: # Set up some docker stuff if args.volumes: # TODO: is volumes list defined here? volumes = volumes.append(genome_outfolder) else: volumes = genome_outfolder if not _writeable(genome_outfolder): _LOGGER.error( "Insufficient permissions to write to output folder: {}". format(genome_outfolder)) return pm = pypiper.PipelineManager(name="refgenie", outfolder=log_outfolder, args=args) tk = pypiper.NGSTk(pm=pm) if args.docker: pm.get_container(build_pkg[CONT], volumes) _LOGGER.debug("Asset build package: " + str(build_pkg)) gat = [genome, asset_key, tag] # create a bundle list to simplify calls below # collect variables required to populate the command templates asset_vars = get_asset_vars(genome, asset_key, tag, genome_outfolder, specific_args, specific_params, **kwargs) # populate command templates # prior to populating, remove any seek_key parts from the keys, since these are not supported by format method command_list_populated = [ x.format(**{k.split(".")[0]: v for k, v in asset_vars.items()}) for x in build_pkg[CMD_LST] ] # create output directory tk.make_dir(asset_vars["asset_outfolder"]) target = os.path.join(log_outfolder, TEMPLATE_TARGET.format(genome, asset_key, tag)) # add target command command_list_populated.append("touch {target}".format(target=target)) _LOGGER.debug("Command populated: '{}'".format( " ".join(command_list_populated))) try: # run build command signal.signal(signal.SIGINT, _handle_sigint(gat)) pm.run(command_list_populated, target, container=pm.container) except pypiper.exceptions.SubprocessError: _LOGGER.error("asset '{}' build failed".format(asset_key)) return False else: # save build recipe to the JSON-formatted file recipe_file_name = TEMPLATE_RECIPE_JSON.format(asset_key, tag) with open(os.path.join(log_outfolder, recipe_file_name), 'w') as outfile: json.dump(build_pkg, outfile) # update and write refgenie genome configuration with rgc as r: r.update_assets(*gat[0:2], data={CFG_ASSET_DESC_KEY: build_pkg[DESC]}) r.update_tags(*gat, data={CFG_ASSET_PATH_KEY: asset_key}) r.update_seek_keys(*gat, keys={ k: v.format(**asset_vars) for k, v in build_pkg[ASSETS].items() }) # in order to conveniently get the path to digest we update the tags metadata in two steps digest = get_dir_digest( r.get_asset(genome, asset_key, tag, enclosing_dir=True), pm) r.update_tags(*gat, data={CFG_ASSET_CHECKSUM_KEY: digest}) _LOGGER.info("Asset digest: {}".format(digest)) r.set_default_pointer(*gat) pm.stop_pipeline() return True for a in asset_list: asset_key = a["asset"] asset_tag = a["tag"] or rgc.get_default_tag( genome, a["asset"], use_existing=False) recipe_name = recipe_name or asset_key if recipe_name in asset_build_packages.keys(): asset_build_package = _check_recipe( asset_build_packages[recipe_name]) # handle user-requested parents for the required assets input_assets = {} parent_assets = [] specified_asset_keys, specified_assets = None, None if args.assets is not None: parsed_parents_input = _parse_user_build_input(args.assets) specified_asset_keys, specified_assets = \ list(parsed_parents_input.keys()), list(parsed_parents_input.values()) _LOGGER.debug("Custom assets requested: {}".format( args.assets)) if not specified_asset_keys and isinstance(args.assets, list): _LOGGER.warning( "Specified parent assets format is invalid. Using defaults." ) for req_asset in asset_build_package[REQ_ASSETS]: req_asset_data = parse_registry_path(req_asset[KEY]) # for each req asset see if non-default parents were requested if specified_asset_keys is not None and req_asset_data[ "asset"] in specified_asset_keys: parent_data = \ parse_registry_path(specified_assets[specified_asset_keys.index(req_asset_data["asset"])]) g, a, t, s = parent_data["genome"], \ parent_data["asset"], \ parent_data["tag"] or rgc.get_default_tag(genome, parent_data["asset"]), \ parent_data["seek_key"] else: # if no custom parents requested for the req asset, use default one default = parse_registry_path(req_asset[DEFAULT]) g, a, t, s = genome, default["asset"], \ rgc.get_default_tag(genome, default["asset"]), \ req_asset_data["seek_key"] parent_assets.append("{}/{}:{}".format(g, a, t)) input_assets[req_asset[KEY]] = _seek(rgc, g, a, t, s) _LOGGER.debug("Using parents: {}".format(", ".join(parent_assets))) _LOGGER.debug("Provided files: {}".format(specified_args)) _LOGGER.debug("Provided parameters: {}".format(specified_params)) for required_file in asset_build_package[REQ_FILES]: if specified_args is None or required_file[ KEY] not in specified_args.keys(): raise ValueError( "Path to the '{x}' input ({desc}) is required, but not provided. " "Specify it with: --files {x}=/path/to/{x}_file". format(x=required_file[KEY], desc=required_file[DESC])) for required_param in asset_build_package[REQ_PARAMS]: if specified_params is None: specified_params = {} if required_param[KEY] not in specified_params.keys(): if required_param[DEFAULT] is None: raise ValueError( "Value for the parameter '{x}' ({desc}) is required, but not provided. " "Specify it with: --params {x}=value".format( x=required_param[KEY], desc=required_param[DESC])) else: specified_params.update( {required_param[KEY]: required_param[DEFAULT]}) genome_outfolder = os.path.join(args.outfolder, genome) _LOGGER.info("Building '{}/{}:{}' using '{}' recipe".format( genome, asset_key, asset_tag, recipe_name)) 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, args.tag_description)) r.update_tags(genome, asset_key, asset_tag, {CFG_TAG_DESC_KEY: args.tag_description}) if recipe_name == "fasta": # to save config lock time when building fasta assets # (genome initialization takes some time for large genomes) we repeat the # conditional here for writing the computed genome digest r.update_genomes( genome, data={CFG_CHECKSUM_KEY: collection_checksum}) else: _raise_missing_recipe_error(recipe_name)