X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b7b9ea44ada30b1251fb10c872cb1da1d7c29bd0..27b732adbd4d2331436a433394658a0cfcf5fd94:/sdk/cwl/arvados_cwl/fsaccess.py

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 548b166c8b..e44e7a9282 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -1,18 +1,20 @@
 import fnmatch
 import os
+import errno
 
-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):
+    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 +22,7 @@ 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)
@@ -82,7 +84,7 @@ class CollectionFsAccess(cwltool.process.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:
@@ -90,11 +92,15 @@ class CollectionFsAccess(cwltool.process.StdFsAccess):
 
     def listdir(self, fn):  # type: (unicode) -> List[unicode]
         collection, rest = self.get_collection(fn)
-        if rest:
-            dir = collection.find(rest)
-        else:
-            dir = collection
         if collection:
+            if rest:
+                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)
@@ -103,3 +109,12 @@ 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)