import fnmatch
import os
-import cwltool.process
+import cwltool.stdfsaccess
from cwltool.pathmapper import abspath
import arvados.util
import arvados.collection
import arvados.arvfile
-class CollectionFsAccess(cwltool.process.StdFsAccess):
+class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
"""Implement the cwltool FsAccess interface for Arvados Collections."""
def __init__(self, basedir, api_client=None):
if paths and paths[-1].startswith("keep:") and arvados.util.keep_locator_pattern.match(paths[-1][5:]):
return paths[-1]
return os.path.join(path, *paths)
+
+ def realpath(self, path):
+ if path.startswith("$(task.tmpdir)") or path.startswith("$(task.outdir)"):
+ return path
+ collection, rest = self.get_collection(path)
+ if collection:
+ return path
+ else:
+ return os.path.realpath(path)