9751: Fix unit tests. Rename dir6.cwl to keep-dir-test-input.cwl

[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..d2589374773e992a440746cc869c8d91eec497cb 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -1,18 +1,19 @@
 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):
+    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)
@@ -103,3 +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)