def construct_tool_object(toolpath_object, *args, **kwargs):
"""Fix missing locations."""
protocol = "file://"
def addLocation(d):
if "location" not in d and "path" in d:
d["location"] = protocol + d["path"]
visit_class(toolpath_object, ("File", "Directory"), addLocation)
return workflow.default_make_tool(toolpath_object, *args, **kwargs)
def construct_tool_object(toolpath_object, *args, **kwargs):
"""Fix missing locations."""
protocol = 'file://'
def addLocation(d):
if 'location' not in d and 'path' in d:
d['location'] = protocol + d['path']
visit_class(toolpath_object, ('File', 'Directory'), addLocation)
return workflow.default_make_tool(toolpath_object, *args, **kwargs)
def calrissian_make_tool(spec, loadingContext):
"""
Construct a Process object from a CWL document loaded into spec
:param spec:
:param loadingContext:
:return: For CommandLineTools, return our specialized subclass that can run on k8s.
For other types of documents, return the CWL default_make_tool
"""
if "class" in spec and spec["class"] == "CommandLineTool":
return CalrissianCommandLineTool(spec, loadingContext)
else:
return default_make_tool(spec, loadingContext)
def make_custom_tool(spec, loading_context, exec_profile_class, workflow_metadata):
"""
custom tool maker:
only use ExecProfileCommandlineTool if spec if the spec is a "CommandLineTool",
otherwise use the cwltool's standard tool maker
"""
if "class" in spec and spec["class"] == "CommandLineTool":
return ExecProfileCommandlineTool(
spec,
loading_context,
exec_profile_class,
workflow_metadata
)
return default_make_tool(spec, loading_context)
def make_tes_tool(spec, loading_context, url):
if "class" in spec and spec["class"] == "CommandLineTool":
return TESCommandLineTool(spec, loading_context, url)
else:
return default_make_tool(spec, loading_context)
def make_tes_tool(spec, loading_context, url, remote_storage_url, token):
"""cwl-tes specific factory for CWL Process generation."""
if "class" in spec and spec["class"] == "CommandLineTool":
return TESCommandLineTool(spec, loading_context, url,
remote_storage_url, token)
return default_make_tool(spec, loading_context)
def make_tool(self, spec, loadingContext):
"""Make tool."""
if "class" in spec and spec["class"] == "CommandLineTool":
return self.make_exec_tool(spec, loadingContext)
else:
return default_make_tool(spec, loadingContext)