[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)
Those revisions listed above that are new to this repository have
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revisions in full, below.
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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