Merge branch '10165-cwl-outputs' closes #10165

[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 0970e72d71d0ce2cef056e05f94bd02ea1324549..89a4308bf14ef2d5f9f3275ddcc4201e749205d8 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -1,5 +1,6 @@
 import fnmatch
 import os
+import errno
 
 import cwltool.stdfsaccess
 from cwltool.pathmapper import abspath
@@ -11,9 +12,10 @@ import arvados.arvfile
 class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
     """Implement the cwltool FsAccess interface for Arvados Collections."""
 
-    def __init__(self, basedir, api_client=None):
+    def __init__(self, basedir, api_client=None, keep_client=None):
         super(CollectionFsAccess, self).__init__(basedir)
         self.api_client = api_client
+        self.keep_client = keep_client
         self.collections = {}
 
     def get_collection(self, path):
@@ -21,7 +23,8 @@ class CollectionFsAccess(cwltool.stdfsaccess.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, api_client=self.api_client)
+                self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client,
+                                                                            keep_client=self.keep_client)
             return (self.collections[pdh], "/".join(p[1:]))
         else:
             return (None, path)
@@ -83,7 +86,7 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
         collection, rest = self.get_collection(fn)
         if collection:
             if rest:
-                return isinstance(collection.find(rest), arvados.collection.Collection)
+                return isinstance(collection.find(rest), arvados.collection.RichCollectionBase)
             else:
                 return True
         else:
@@ -96,6 +99,10 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
                 dir = collection.find(rest)
             else:
                 dir = collection
+            if dir is None:
+                raise IOError(errno.ENOENT, "Directory '%s' in '%s' not found" % (rest, collection.portable_data_hash()))
+            if not isinstance(dir, arvados.collection.RichCollectionBase):
+                raise IOError(errno.ENOENT, "Path '%s' in '%s' is not a Directory" % (rest, collection.portable_data_hash()))
             return [abspath(l, fn) for l in dir.keys()]
         else:
             return super(CollectionFsAccess, self).listdir(fn)