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Source code for galaxy.tools.cwl.cwltool_deps

"""Logic for dealing with cwltool as an optional dependency.

Use this as the import interface for cwltool and just call
:func:`ensure_cwltool_available` before using any of the imported
functionality at runtime.
"""
import re

try:
    import requests
except ImportError:
    requests = None

try:
    from cwltool import (
        main,
        workflow,
        job,
        process,
        pathmapper,
    )
except (ImportError, SyntaxError):
    # Drop SyntaxError once cwltool supports Python 3
    main = None
    workflow = None
    job = None
    process = None
    pathmapper = None

try:
    from cwltool.context import LoadingContext  # Introduced in cwltool 1.0.20180615183820
except (ImportError, SyntaxError):
    LoadingContext = None

try:
    from cwltool import load_tool
except (ImportError, SyntaxError):
    load_tool = None

try:
    import shellescape
except ImportError:
    shellescape = None

try:
    import schema_salad
except (ImportError, SyntaxError):
    # Drop SyntaxError once schema_salad supports Python 3
    schema_salad = None

try:
    from schema_salad import ref_resolver
except (ImportError, SyntaxError):
    ref_resolver = None


needs_shell_quoting = re.compile(r"""(^$|[\s|&;()<>\'"$@])""").search


[docs]def ensure_cwltool_available(): """Assert optional dependencies proxied via this module are available at runtime. Throw an ImportError with a description of the problem if they do not exist. """ if main is None or workflow is None or shellescape is None: message = "This feature requires cwltool and dependencies to be available, they are not." if main is None: message += " cwltool is not unavailable." elif load_tool is None: message += " cwltool.load_tool is unavailable - cwltool version is too old." if requests is None: message += " Library 'requests' unavailable." if shellescape is None: message += " Library 'shellescape' unavailable." if schema_salad is None: message += " Library 'schema_salad' unavailable." raise ImportError(message)
__all__ = ( 'main', 'ref_resolver', 'load_tool', 'LoadingContext', 'workflow', 'process', 'pathmapper', 'ensure_cwltool_available', 'schema_salad', 'shellescape', 'needs_shell_quoting', )