[ARVADOS] updated: 0d2a561091b777dfb7735d842a88f8529f4f982a

Git user git at public.curoverse.com
Mon Nov 7 17:03:07 EST 2016


Summary of changes:
 build/run-build-packages.sh       |  2 +-
 sdk/cwl/arvados_cwl/__init__.py   | 36 ++++++++++++++++++++++++++++--------
 sdk/cwl/arvados_cwl/pathmapper.py | 13 +++++++++----
 sdk/cwl/setup.py                  |  2 +-
 sdk/cwl/tests/test_make_output.py |  2 +-
 5 files changed, 40 insertions(+), 15 deletions(-)

       via  0d2a561091b777dfb7735d842a88f8529f4f982a (commit)
       via  dac167d2d3d259de8fd70d1289dbbe65c7974d4a (commit)
       via  c863f911c9a55203bbe0bd3735162084b94f582f (commit)
       via  ac9e30c830fd8acdd04ff2a8067f3b33d95325f5 (commit)
      from  928c4a5b8d3645994d99c881914bcf1683e69d1d (commit)

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commit 0d2a561091b777dfb7735d842a88f8529f4f982a
Merge: 928c4a5 dac167d
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Nov 7 17:03:00 2016 -0500

    Merge branch '10460-cwl-directory-literal' closes #10460


commit dac167d2d3d259de8fd70d1289dbbe65c7974d4a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Nov 7 17:02:18 2016 -0500

    10460: Style tweak make_output_collection

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index c221a32..5ae2de3 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -254,8 +254,7 @@ class ArvCwlRunner(object):
         adjustDirObjs(outputObj, finalcollection)
         adjustFileObjs(outputObj, finalcollection)
 
-        self.final_output_collection = final
-        return outputObj
+        return (outputObj, final)
 
     def set_crunch_output(self):
         if self.work_api == "containers":
@@ -411,7 +410,7 @@ class ArvCwlRunner(object):
         else:
             if self.output_name is None:
                 self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
-            self.final_output = self.make_output_collection(self.output_name, self.final_output)
+            self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.final_output)
             self.set_crunch_output()
 
         if self.final_status != "success":
diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 15685fc..c15b289 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -195,7 +195,7 @@ class FinalOutputPathMapper(PathMapper):
         elif obj["class"] == "File":
             if loc in self._pathmap:
                 return
-            if "contents" in obj and obj["location"].startswith("_:"):
+            if "contents" in obj and loc.startswith("_:"):
                 self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile")
             else:
                 self._pathmap[loc] = MapperEnt(loc, tgt, "File")
diff --git a/sdk/cwl/tests/test_make_output.py b/sdk/cwl/tests/test_make_output.py
index 0b08b2e..776f07c 100644
--- a/sdk/cwl/tests/test_make_output.py
+++ b/sdk/cwl/tests/test_make_output.py
@@ -32,7 +32,7 @@ class TestMakeOutput(unittest.TestCase):
         final.open.return_value = openmock
         openmock.__enter__.return_value = cwlout
 
-        runner.make_output_collection("Test output", {
+        _, runner.final_output_collection = runner.make_output_collection("Test output", {
             "foo": {
                 "class": "File",
                 "location": "keep:99999999999999999999999999999991+99/foo.txt",

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