Add realpath() to FsAccess interface. (#160)

* Add realpath() to FsAccess interface.

* Remove spurious print.

Author: tetron

cwltool/process.py

@@ -419,18 +419,18 @@ def _init_job(self, joborder, **kwargs):
         if dockerReq and is_req and not kwargs.get("use_container"):
             raise WorkflowException("Document has DockerRequirement under 'requirements' but use_container is false.  DockerRequirement must be under 'hints' or use_container must be true.")
 
-        if dockerReq and kwargs.get("use_container"):
-            builder.outdir = os.path.realpath(kwargs.get("docker_outdir") or "/var/spool/cwl")
-            builder.tmpdir = os.path.realpath(kwargs.get("docker_tmpdir") or "/tmp")
-            builder.stagedir = os.path.realpath(kwargs.get("docker_stagedir") or "/var/lib/cwl")
-        else:
-            builder.outdir = os.path.realpath(kwargs.get("outdir") or tempfile.mkdtemp())
-            builder.tmpdir = os.path.realpath(kwargs.get("tmpdir") or tempfile.mkdtemp())
-            builder.stagedir = os.path.realpath(kwargs.get("stagedir") or tempfile.mkdtemp())
-
         builder.make_fs_access = kwargs.get("make_fs_access") or StdFsAccess
         builder.fs_access = builder.make_fs_access(kwargs["basedir"])
 
+        if dockerReq and kwargs.get("use_container"):
+            builder.outdir = builder.fs_access.realpath(kwargs.get("docker_outdir") or "/var/spool/cwl")
+            builder.tmpdir = builder.fs_access.realpath(kwargs.get("docker_tmpdir") or "/tmp")
+            builder.stagedir = builder.fs_access.realpath(kwargs.get("docker_stagedir") or "/var/lib/cwl")
+        else:
+            builder.outdir = builder.fs_access.realpath(kwargs.get("outdir") or tempfile.mkdtemp())
+            builder.tmpdir = builder.fs_access.realpath(kwargs.get("tmpdir") or tempfile.mkdtemp())
+            builder.stagedir = builder.fs_access.realpath(kwargs.get("stagedir") or tempfile.mkdtemp())
+
         if self.formatgraph:
             for i in self.tool["inputs"]:
                 d = shortname(i["id"])

cwltool/stdfsaccess.py

@@ -32,3 +32,6 @@ def listdir(self, fn):  # type: (unicode) -> List[unicode]
 
     def join(self, path, *paths): # type: (unicode, *unicode) -> unicode
         return os.path.join(path, *paths)
+
+    def realpath(self, path):
+        return os.path.realpath(path)