X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5603cefb38fbd2fc6493e8ccee587629e7af089e..6e0abcdabb14bcd21695420d3cfab0d57362a2be:/sdk/cwl/arvados_cwl/fsaccess.py

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 661a9e0868..d258937477 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -1,14 +1,14 @@
 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):
@@ -17,7 +17,6 @@ class CollectionFsAccess(cwltool.process.StdFsAccess):
         self.collections = {}
 
     def get_collection(self, path):
-        print "PPP", path
         p = path.split("/")
         if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]):
             pdh = p[0][5:]
@@ -105,3 +104,12 @@ class CollectionFsAccess(cwltool.process.StdFsAccess):
         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)