def get_file_dependencies_obj(cwl_obj, basedir):
"""Return a dictionary which contains the CWL workflow file dependencies.
:param cwl_obj: A CWL tool or job which might contain file dependencies.
:param basedir: Workflow base dir.
:returns: A dictionary composed of valid CWL file dependencies.
"""
# Load the document
# remove filename additions (e.g. 'v1.0/conflict-wf.cwl#collision')
document = cwl_obj.split("#")[0]
document_loader, workflow_obj, uri = fetch_document(document)
in_memory_buffer = io.StringIO()
# Get dependencies
printdeps(
workflow_obj,
document_loader.loader,
in_memory_buffer,
"primary",
uri,
basedir=basedir,
)
file_dependencies_obj = yaml.load(in_memory_buffer.getvalue(),
Loader=yaml.FullLoader)
in_memory_buffer.close()
return file_dependencies_obj
def get_file_dependencies_obj(cwl_obj, basedir):
"""Return a dictionary which contains the CWL workflow file dependencies.
:param cwl_obj: A CWL tool or job which might contain file dependencies.
:param basedir: Workflow base dir.
:returns: A dictionary composed of valid CWL file dependencies.
"""
# Load de document
loading_context = LoadingContext()
document_loader, workflow_obj, uri = fetch_document(
cwl_obj,
resolver=loading_context.resolver,
fetcher_constructor=loading_context.fetcher_constructor,
)
in_memory_buffer = io.StringIO() if PY3 else io.BytesIO()
# Get dependencies
printdeps(workflow_obj,
document_loader,
in_memory_buffer,
"primary",
uri,
basedir=basedir)
file_dependencies_obj = yaml.load(in_memory_buffer.getvalue(),
Loader=yaml.FullLoader)
in_memory_buffer.close()
return file_dependencies_obj