[ARVADOS] updated: a677caec8b7bc236d9558ff39913237a3e4ed8fc

Git user git at public.curoverse.com
Fri Mar 11 09:45:27 EST 2016


Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py                    |  5 +-
 sdk/cwl/setup.py                                   |  2 +-
 sdk/cwl/tests/test_job.py                          |  8 +-
 .../arvados/v1/repositories_controller.rb          |  4 +-
 .../arvados/v1/repositories_controller_test.rb     |  4 +-
 services/arv-git-httpd/gitolite_test.go            | 14 +++-
 services/crunch-run/crunchrun_test.go              | 61 +++++++++-------
 services/crunch-run/logging_test.go                | 12 +--
 services/datamanager/datamanager.go                |  2 +-
 services/datamanager/datamanager_test.go           | 26 ++++++-
 services/nodemanager/arvnodeman/baseactor.py       | 85 ++++++++++++++++++++++
 services/nodemanager/arvnodeman/clientactor.py     |  2 +-
 .../arvnodeman/computenode/dispatch/__init__.py    | 11 ++-
 services/nodemanager/arvnodeman/config.py          |  4 +-
 services/nodemanager/arvnodeman/daemon.py          | 21 +++---
 services/nodemanager/arvnodeman/fullstopactor.py   | 17 -----
 services/nodemanager/arvnodeman/launcher.py        | 12 +--
 services/nodemanager/arvnodeman/timedcallback.py   |  2 +-
 services/nodemanager/tests/test_daemon.py          |  1 +
 services/nodemanager/tests/test_failure.py         | 29 +++-----
 services/nodemanager/tests/testutil.py             |  5 +-
 21 files changed, 214 insertions(+), 113 deletions(-)
 create mode 100644 services/nodemanager/arvnodeman/baseactor.py
 delete mode 100644 services/nodemanager/arvnodeman/fullstopactor.py

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commit a677caec8b7bc236d9558ff39913237a3e4ed8fc
Merge: b4c4d4c d1de328
Author: radhika <radhika at curoverse.com>
Date:   Fri Mar 11 09:45:17 2016 -0500

    Merge branch 'master' into 8558-cwl-propagate-resource-req
    
    Conflicts:
    	sdk/cwl/arvados_cwl/__init__.py

diff --cc sdk/cwl/setup.py
index b85f3b4,cacfc21..1deb766
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@@ -30,11 -30,9 +30,11 @@@ setup(name='arvados-cwl-runner'
            'bin/arvados-cwl-runner'
        ],
        install_requires=[
-           'cwltool>=1.0.20160302134341',
+           'cwltool>=1.0.20160308152645',
            'arvados-python-client>=0.1.20160219154918'
        ],
 +      test_suite='tests',
 +      tests_require=['mock>=1.0'],
        zip_safe=True,
        cmdclass={'egg_info': tagger},
        )
diff --cc sdk/cwl/tests/test_job.py
index 9a1f9ec,0000000..0b38db2
mode 100644,000000..100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@@ -1,77 -1,0 +1,77 @@@
 +import unittest
 +import mock
 +import arvados_cwl
 +
 +class TestJob(unittest.TestCase):
 +
 +    # The test passes no builder.resources
 +    # Hence the default resources will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 +    def test_run(self):
 +        runner = mock.MagicMock()
 +        tool = {
 +            "inputs": [],
 +            "outputs": [],
 +            "baseCommand": "ls"
 +        }
 +        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool)
 +        arvtool.formatgraph = None
 +        for j in arvtool.job({}, "", mock.MagicMock()):
 +            j.run()
 +        runner.api.jobs().create.assert_called_with(body={
 +            'runtime_constraints': {},
 +            'script_parameters': {
 +                'tasks': [{
 +                    'task.env': {'TMPDIR': '$(task.tmpdir)'},
 +                    'command': ['ls']
 +                }],
 +                'crunchrunner': '83db29f08544e1c319572a6bd971088a+140/crunchrunner'
 +            },
-             'script_version':
-             'master',
++            'script_version': 'master',
++            'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 +            'repository': 'arvados',
 +            'script': 'crunchrunner',
 +            'runtime_constraints': {
 +                'min_cores_per_node': 1,
 +                'min_ram_mb_per_node': 1024,
 +                'min_scratch_mb_per_node': 2048 # tmpdirSize + outdirSize
 +            }
 +        }, find_or_create=True)
 +
 +    # The test passes some fields in builder.resources
 +    # For the remaining fields, the defaults will apply: {'cores': 1, 'ram': 1024, 'outdirSize': 1024, 'tmpdirSize': 1024}
 +    def test_resource_requirements(self):
 +        runner = mock.MagicMock()
 +        tool = {
 +            "inputs": [],
 +            "outputs": [],
 +            "hints": [{
 +                "class": "ResourceRequirement",
 +                "coresMin": 3,
 +                "ramMin": 3000,
 +                "tmpdirMin": 4000
 +            }],
 +            "baseCommand": "ls"
 +        }
 +        arvtool = arvados_cwl.ArvadosCommandTool(runner, tool)
 +        arvtool.formatgraph = None
 +        for j in arvtool.job({}, "", mock.MagicMock()):
 +            j.run()
 +        runner.api.jobs().create.assert_called_with(body={
 +            'runtime_constraints': {},
 +            'script_parameters': {
 +                'tasks': [{
 +                    'task.env': {'TMPDIR': '$(task.tmpdir)'},
 +                    'command': ['ls']
 +                }],
 +                'crunchrunner': '83db29f08544e1c319572a6bd971088a+140/crunchrunner'
 +            },
-             'script_version':
-             'master',
++            'script_version': 'master',
++            'minimum_script_version': '9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
 +            'repository': 'arvados',
 +            'script': 'crunchrunner',
 +            'runtime_constraints': {
 +                'min_cores_per_node': 3,
 +                'min_ram_mb_per_node': 3000,
 +                'min_scratch_mb_per_node': 5024 # tmpdirSize + outdirSize
 +            }
 +        }, find_or_create=True)

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