X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/779c5400a4f376489f4abc8564f890f309ae3f20..8d61948fecccfc60db2f18ba4daf7c01ddf3d3c8:/sdk/cwl/arvados_cwl/pathmapper.py

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index fb4ae5ad45..40a64ffd20 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -1,6 +1,7 @@
 import re
 import logging
 import uuid
+import os
 
 import arvados.commands.run
 import arvados.collection
@@ -51,13 +52,14 @@ class ArvPathMapper(PathMapper):
         elif srcobj["class"] == "Directory":
             if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
                 self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "Directory")
-            else:
-                for l in srcobj["listing"]:
-                    self.visit(l, uploadfiles)
+            for l in srcobj["listing"]:
+                self.visit(l, uploadfiles)
 
     def addentry(self, obj, c, path, subdirs):
         if obj["location"] in self._pathmap:
             src, srcpath = self.arvrunner.fs_access.get_collection(self._pathmap[obj["location"]].resolved)
+            if srcpath == "":
+                srcpath = "."
             c.copy(srcpath, path + "/" + obj["basename"], source_collection=src, overwrite=True)
             for l in obj.get("secondaryFiles", []):
                 self.addentry(l, c, path, subdirs)
@@ -142,6 +144,26 @@ class ArvPathMapper(PathMapper):
             return super(ArvPathMapper, self).reversemap(target)
 
 class InitialWorkDirPathMapper(PathMapper):
+
+    def visit(self, obj, stagedir, basedir, copy=False):
+        # type: (Dict[unicode, Any], unicode, unicode, bool) -> None
+        if obj["class"] == "Directory":
+            self._pathmap[obj["location"]] = MapperEnt(obj["location"], stagedir, "Directory")
+            self.visitlisting(obj.get("listing", []), stagedir, basedir)
+        elif obj["class"] == "File":
+            loc = obj["location"]
+            if loc in self._pathmap:
+                return
+            tgt = os.path.join(stagedir, obj["basename"])
+            if "contents" in obj and obj["location"].startswith("_:"):
+                self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile")
+            else:
+                if copy:
+                    self._pathmap[loc] = MapperEnt(obj["path"], tgt, "WritableFile")
+                else:
+                    self._pathmap[loc] = MapperEnt(obj["path"], tgt, "File")
+                self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir)
+
     def setup(self, referenced_files, basedir):
         # type: (List[Any], unicode) -> None