9552: add compute-checksum flag to arvados-cwl-runner

[arvados.git] / sdk / cwl / arvados_cwl / fsaccess.py

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 548b166c8b0dff5e902bd315c5e4fd4005c71c66..d2d38b00c35a89f2a1a1f179a0468b821e48670a 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -11,8 +11,9 @@ import arvados.arvfile
 class CollectionFsAccess(cwltool.process.StdFsAccess):
     """Implement the cwltool FsAccess interface for Arvados Collections."""
 
-    def __init__(self, basedir):
+    def __init__(self, basedir, api_client=None):
         super(CollectionFsAccess, self).__init__(basedir)
+        self.api_client = api_client
         self.collections = {}
 
     def get_collection(self, path):
@@ -20,7 +21,7 @@ class CollectionFsAccess(cwltool.process.StdFsAccess):
         if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]):
             pdh = p[0][5:]
             if pdh not in self.collections:
-                self.collections[pdh] = arvados.collection.CollectionReader(pdh)
+                self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client)
             return (self.collections[pdh], "/".join(p[1:]))
         else:
             return (None, path)