[ARVADOS] updated: cdfd69a42adf6ed017a443773eccfd8f021fea32

[git at public.curoverse.com]

Summary of changes:
 sdk/cwl/arvados_cwl/{cwl_runner.py => __init__.py} | 4 ++--
 sdk/cwl/bin/cwl-runner                             | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)
 rename sdk/cwl/arvados_cwl/{cwl_runner.py => __init__.py} (99%)

       via  cdfd69a42adf6ed017a443773eccfd8f021fea32 (commit)
      from  50abee31d6dad724c0d4b8a452eeb330364cde85 (commit)

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commit cdfd69a42adf6ed017a443773eccfd8f021fea32
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Jul 6 22:31:35 2015 -0400

    6264: Fix bin/cwl-runner to import correct module.

diff --git a/sdk/cwl/arvados_cwl/cwl_runner.py b/sdk/cwl/arvados_cwl/__init__.py
similarity index 99%
rename from sdk/cwl/arvados_cwl/cwl_runner.py
rename to sdk/cwl/arvados_cwl/__init__.py
index 65f4940..052ace9 100644
--- a/sdk/cwl/arvados_cwl/cwl_runner.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -99,7 +99,7 @@ class ArvadosJob(object):
             vwd = arvados.collection.Collection()
             for t in self.generatefiles:
                 if isinstance(self.generatefiles[t], dict):
-                    src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"][7:-1])
+                    src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"][6:])
                     vwd.copy(rest, t, source_collection=src)
                 else:
                     with vwd.open(t, "w") as f:
@@ -165,7 +165,7 @@ class ArvPathMapper(cwltool.pathmapper.PathMapper):
 
         for src in referenced_files:
             if isinstance(src, basestring) and pdh_path.match(src):
-                self._pathmap[src] = (src, "$(file %s)" % src)
+                self._pathmap[src] = (src, "/keep/%s" % src)
             else:
                 ab = src if os.path.isabs(src) else os.path.join(basedir, src)
                 st = arvados.commands.run.statfile("", ab)
diff --git a/sdk/cwl/bin/cwl-runner b/sdk/cwl/bin/cwl-runner
index 7008ae4..f31aefd 100755
--- a/sdk/cwl/bin/cwl-runner
+++ b/sdk/cwl/bin/cwl-runner
@@ -2,6 +2,6 @@
 
 import sys
 
-from arvados.commands.cwl_runner import main
+from arvados_cwl import main
 
 sys.exit(main(sys.argv[1:], sys.stdout, sys.stderr))

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