diff --git a/lib/galaxy/tool_util/cwl/__init__.py b/lib/galaxy/tool_util/cwl/__init__.py index bb55b897519e..e932c0fa725e 100644 --- a/lib/galaxy/tool_util/cwl/__init__.py +++ b/lib/galaxy/tool_util/cwl/__init__.py @@ -1,7 +1,4 @@ -from .cwltool_deps import ( - needs_shell_quoting, - shellescape, -) +from .cwltool_deps import needs_shell_quoting from .parser import ( tool_proxy, tool_proxy_from_persistent_representation, @@ -21,5 +18,4 @@ "to_cwl_job", "to_galaxy_parameters", "needs_shell_quoting", - "shellescape", ) diff --git a/lib/galaxy/tool_util/cwl/cwltool_deps.py b/lib/galaxy/tool_util/cwl/cwltool_deps.py index 9d0bba1d5393..78abdd08e232 100644 --- a/lib/galaxy/tool_util/cwl/cwltool_deps.py +++ b/lib/galaxy/tool_util/cwl/cwltool_deps.py @@ -4,6 +4,7 @@ :func:`ensure_cwltool_available` before using any of the imported functionality at runtime. """ + import re import warnings @@ -70,11 +71,6 @@ visit_class = None # type: ignore[assignment] normalizeFilesDirs = None # type: ignore[assignment] -try: - import shellescape -except ImportError: - shellescape = None - try: import schema_salad from schema_salad import ( @@ -104,7 +100,7 @@ def ensure_cwltool_available(): 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: + if main is None or workflow is None: message = "This feature requires cwltool and dependencies to be available, they are not." if main is None: message += " cwltool is not unavailable." @@ -112,8 +108,6 @@ def ensure_cwltool_available(): message += " cwltool.load_tool.resolve_and_validate_document 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) @@ -136,7 +130,6 @@ def ensure_cwltool_available(): "resolve_and_validate_document", "RuntimeContext", "schema_salad", - "shellescape", "sourceline", "StdFsAccess", "visit_class",