From 1ca3b77ff42e1bfa0076a27bba1daa0406655082 Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curoverse.com>
Date: Thu, 28 Jan 2016 16:41:08 -0500
Subject: [PATCH] 8319: Fix arv-cwl-runner file references when referencing
 files in Keep.

---
 sdk/cwl/arvados_cwl/__init__.py    | 5 +++--
 sdk/python/arvados/commands/run.py | 6 +++---
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 4198c34482..cf18894eaa 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -166,7 +166,8 @@ class ArvadosJob(object):
 
             try:
                 outputs = {}
-                outputs = self.collect_outputs("keep:" + record["output"])
+                if record["output"]:
+                    outputs = self.collect_outputs("keep:" + record["output"])
             except Exception as e:
                 logger.exception("Got exception while collecting job outputs:")
                 processStatus = "permanentFail"
@@ -188,7 +189,7 @@ class ArvPathMapper(cwltool.pathmapper.PathMapper):
                 self._pathmap[src] = (src, "$(task.keep)/%s" % src[5:])
             if src not in self._pathmap:
                 ab = cwltool.pathmapper.abspath(src, basedir)
-                st = arvados.commands.run.statfile("", ab)
+                st = arvados.commands.run.statfile("", ab, fnPattern="$(task.keep)/%s/%s")
                 if kwargs.get("conformance_test"):
                     self._pathmap[src] = (src, ab)
                 elif isinstance(st, arvados.commands.run.UploadFile):
diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index 5c8bced513..ef39be81a4 100644
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -81,7 +81,7 @@ def determine_project(root, current_user):
 # ArvFile() (file already exists in a collection), UploadFile() (file needs to
 # be uploaded to a collection), or simply returns prefix+fn (which yields the
 # original parameter string).
-def statfile(prefix, fn):
+def statfile(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
     absfn = os.path.abspath(fn)
     if os.path.exists(absfn):
         st = os.stat(absfn)
@@ -89,7 +89,7 @@ def statfile(prefix, fn):
             sp = os.path.split(absfn)
             (pdh, branch) = is_in_collection(sp[0], sp[1])
             if pdh:
-                return ArvFile(prefix, "$(file %s/%s)" % (pdh, branch))
+                return ArvFile(prefix, fnPattern % (pdh, branch))
             else:
                 # trim leading '/' for path prefix test later
                 return UploadFile(prefix, absfn[1:])
@@ -97,7 +97,7 @@ def statfile(prefix, fn):
             sp = os.path.split(absfn)
             (pdh, branch) = is_in_collection(sp[0], sp[1])
             if pdh:
-                return ArvFile(prefix, "$(dir %s/%s/)" % (pdh, branch))
+                return ArvFile(prefix, dirPattern % (pdh, branch))
 
     return prefix+fn
 
-- 
2.39.5