def get_tool_source(config_file=None, xml_tree=None, enable_beta_formats=True, tool_location_fetcher=None): """Return a ToolSource object corresponding to supplied source. The supplied source may be specified as a file path (using the config_file parameter) or as an XML object loaded with load_tool_xml. """ if xml_tree is not None: return XmlToolSource(xml_tree, source_path=config_file) elif config_file is None: raise ValueError("get_tool_source called with invalid config_file None.") if tool_location_fetcher is None: tool_location_fetcher = ToolLocationFetcher() config_file = tool_location_fetcher.to_tool_path(config_file) if not enable_beta_formats: tree = load_tool_xml(config_file) return XmlToolSource(tree, source_path=config_file) if config_file.endswith(".yml"): log.info("Loading tool from YAML - this is experimental - tool will not function in future.") with open(config_file, "r") as f: as_dict = ordered_load(f) return YamlToolSource(as_dict, source_path=config_file) elif config_file.endswith(".json") or config_file.endswith(".cwl"): log.info("Loading CWL tool - this is experimental - tool likely will not function in future at least in same way.") return CwlToolSource(config_file) else: tree = load_tool_xml(config_file) return XmlToolSource(tree, source_path=config_file)
def get_tool_source(config_file=None, xml_tree=None, enable_beta_formats=True): """Return a ToolSource object corresponding to supplied source. The supplied source may be specified as a file path (using the config_file parameter) or as an XML object loaded with load_tool_xml. """ if xml_tree is not None: return XmlToolSource(xml_tree, source_path=config_file) elif config_file is None: raise ValueError("get_tool_source called with invalid config_file None.") if not enable_beta_formats: tree = load_tool_xml(config_file) return XmlToolSource(tree, source_path=config_file) if config_file.endswith(".yml"): log.info("Loading tool from YAML - this is experimental - tool will not function in future.") with open(config_file, "r") as f: as_dict = ordered_load(f) return YamlToolSource(as_dict, source_path=config_file) elif config_file.endswith(".json") or config_file.endswith(".cwl"): log.info("Loading CWL tool - this is experimental - tool likely will not function in future at least in same way.") return CwlToolSource(config_file) else: tree = load_tool_xml(config_file) return XmlToolSource(tree, source_path=config_file)
def get_tool_source(config_file, enable_beta_formats=True): if not enable_beta_formats: tree = load_tool_xml(config_file) root = tree.getroot() return XmlToolSource(root) if config_file.endswith(".yml"): log.info("Loading tool from YAML - this is experimental - tool will not function in future.") with open(config_file, "r") as f: as_dict = yaml.load(f) return YamlToolSource(as_dict) else: tree = load_tool_xml(config_file) root = tree.getroot() return XmlToolSource(root)
def get_tool_source(config_file, enable_beta_formats=True): if not enable_beta_formats: tree = load_tool_xml(config_file) root = tree.getroot() return XmlToolSource(root) if config_file.endswith(".yml"): log.info( "Loading tool from YAML - this is experimental - tool will not function in future." ) with open(config_file, "r") as f: as_dict = yaml.load(f) return YamlToolSource(as_dict) else: tree = load_tool_xml(config_file) root = tree.getroot() return XmlToolSource(root)
def get_tool_source(config_file, enable_beta_formats=True): if not enable_beta_formats: tree = load_tool_xml(config_file) root = tree.getroot() return XmlToolSource(root) if config_file.endswith(".yml"): log.info("Loading tool from YAML - this is experimental - tool will not function in future.") with open(config_file, "r") as f: as_dict = ordered_load(f) return YamlToolSource(as_dict) elif config_file.endswith(".json") or config_file.endswith(".cwl"): log.info("Loading CWL tool - this is experimental - tool likely will not function in future at least in same way.") return CwlToolSource(config_file) else: tree = load_tool_xml(config_file) root = tree.getroot() return XmlToolSource(root)
def get_tool_source(config_file, enable_beta_formats=True): if not enable_beta_formats: tree = load_tool_xml(config_file) root = tree.getroot() return XmlToolSource(root, source_path=config_file) if config_file.endswith(".yml"): log.info("Loading tool from YAML - this is experimental - tool will not function in future.") with open(config_file, "r") as f: as_dict = ordered_load(f) return YamlToolSource(as_dict, source_path=config_file) elif config_file.endswith(".json") or config_file.endswith(".cwl"): log.info("Loading CWL tool - this is experimental - tool likely will not function in future at least in same way.") return CwlToolSource(config_file) else: tree = load_tool_xml(config_file) root = tree.getroot() return XmlToolSource(root, source_path=config_file)