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 65f4940e1be428836c29bdeae2cc73a876929093..052ace930b33fb5e050de3b86f8a32643c68d8a6 100644 (file)
--- 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 7008ae499087f0773782be8752d34498d6f7c582..f31aefdf2efc5fb4a6a00dbc382b22b876909bbb 100755 (executable)
--- 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))