Python load_tool_xml示例

示例#1

文件： factory.py 项目： ashvark/galaxy

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)

示例#2

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)

示例#3

文件： factory.py 项目： brandeis-nlp/Galaxy

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)

示例#4

文件： factory.py 项目： odoppelt/galaxy-central

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)

示例#5

文件： factory.py 项目： AbhishekKumarSingh/galaxy

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)

示例#6

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)