[ARVADOS] updated: d5436dcc5038e93538e36ad918acec2357865202

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py |  5 +++++
 sdk/cwl/tests/test_submit.py    | 10 +++++-----
 2 files changed, 10 insertions(+), 5 deletions(-)

       via  d5436dcc5038e93538e36ad918acec2357865202 (commit)
       via  efa02bcc16b313cc8ff830944ada33eb8b2b2189 (commit)
      from  cb214c45eceb71882e47f619eb5233d83fd949f4 (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
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commit d5436dcc5038e93538e36ad918acec2357865202
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jan 17 16:54:13 2017 -0500

    10812: Test fixes

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 1b52fb5..8b3db8f 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -124,7 +124,7 @@ def stubs(func):
                     'class': 'Directory'
                 },
                 'cwl:tool':
-                'f57578d5cfda7f70fef00cbc4b621e6b+58/workflow.cwl'
+                'f57578d5cfda7f70fef00cbc4b621e6b+58/workflow.cwl#main'
             },
             'repository': 'arvados',
             'script_version': 'master',
@@ -146,7 +146,7 @@ def stubs(func):
                               'listing': [
                                   {'basename': 'renamed.txt', 'class': 'File', 'location': 'keep:99999999999999999999999999999998+99/file1.txt'}
                               ]}},
-                        'cwl:tool': 'f57578d5cfda7f70fef00cbc4b621e6b+58/workflow.cwl',
+                        'cwl:tool': 'f57578d5cfda7f70fef00cbc4b621e6b+58/workflow.cwl#main',
                         'arv:enable_reuse': True,
                         'arv:on_error': 'continue'
                     },
@@ -180,7 +180,7 @@ def stubs(func):
                     'kind': 'collection'
                 },
                 '/var/lib/cwl/workflow.json': {
-                    'json': expect_packed_workflow,
+                    'content': expect_packed_workflow,
                     'kind': 'json'
                 },
                 'stdout': {
@@ -680,7 +680,7 @@ class TestSubmit(unittest.TestCase):
                 },
                 '/var/lib/cwl/workflow.json': {
                     'kind': 'json',
-                    'json': {
+                    'content': {
                         'cwlVersion': 'v1.0',
                         '$graph': [
                             {
@@ -1080,7 +1080,7 @@ class TestTemplateInputs(unittest.TestCase):
                 },
                 'script_parameters': {
                     'cwl:tool':
-                    '5800682d508698dc9ce6d2fc618f21d8+58/workflow.cwl',
+                    '5800682d508698dc9ce6d2fc618f21d8+58/workflow.cwl#main',
                     'optionalFloatInput': None,
                     'fileInput': {
                         'type': 'File',

commit efa02bcc16b313cc8ff830944ada33eb8b2b2189
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Jan 16 10:51:10 2017 -0500

    10812: Check for dockerOutputDirectory and raise UnsupportedRequirement up front.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index a5fa4e0..a0c9d57 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -211,6 +211,11 @@ class ArvCwlRunner(object):
                         raise SourceLine(obj, "stdin", UnsupportedRequirement).makeError("Stdin redirection currently not suppported with --api=containers")
                     if obj.get("stderr"):
                         raise SourceLine(obj, "stderr", UnsupportedRequirement).makeError("Stderr redirection currently not suppported with --api=containers")
+            if obj.get("class") == "DockerRequirement":
+                if obj.get("dockerOutputDirectory"):
+                    # TODO: can be supported by containers API, but not jobs API.
+                    raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError(
+                        "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
             for v in obj.itervalues():
                 self.check_features(v)
         elif isinstance(obj, list):

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