[ARVADOS] updated: 1.2.0-18-g3c08b21fd
Git user
git at public.curoverse.com
Wed Sep 12 16:15:27 EDT 2018
Summary of changes:
doc/api/methods/containers.html.textile.liquid | 1 -
sdk/cwl/arvados_cwl/__init__.py | 6 ++---
sdk/cwl/tests/test_container.py | 34 ++++++++++++++++++++------
3 files changed, 28 insertions(+), 13 deletions(-)
via 3c08b21fd2d0b07094554f6761eac799cfc31ea0 (commit)
via 8674cfd50ad24171de7d157813819f3383c3353b (commit)
from 21810ed18611adbb902bc7dc35407fc4e4adc828 (commit)
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commit 3c08b21fd2d0b07094554f6761eac799cfc31ea0
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date: Wed Sep 12 17:14:41 2018 -0300
13773: Update test that confirms runtime_status is updated when a child fails
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 5ea402a66..94615bbcb 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -236,10 +236,8 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
def runtime_status_update(self, kind, message, detail=None):
"""
Updates the runtime_status field on the runner container.
- Called from a failing child container: records the first child error
- or updates the error count on subsequent error statuses.
- Also called from other parts that need to report errros, warnings or just
- activity statuses.
+ Called when there's a need to report errors, warnings or just
+ activity statuses, for example in the RuntimeStatusLoggingHandler.
"""
with self.workflow_eval_lock:
current = get_current_container(self.api, self.num_retries, logger)
diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index 9bac3184f..4976515da 100644
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -5,6 +5,7 @@
import arvados_cwl
import arvados_cwl.context
from arvados_cwl.arvdocker import arv_docker_clear_cache
+import copy
import arvados.config
import logging
import mock
@@ -17,6 +18,7 @@ from schema_salad.ref_resolver import Loader
from schema_salad.sourceline import cmap
from .matcher import JsonDiffMatcher
+from .mock_discovery import get_rootDesc
if not os.getenv('ARVADOS_DEBUG'):
logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
@@ -494,19 +496,36 @@ class TestContainer(unittest.TestCase):
arvjob.output_callback.assert_called_with({"out": "stuff"}, "success")
runner.add_intermediate_output.assert_called_with("zzzzz-4zz18-zzzzzzzzzzzzzz2")
- @mock.patch("arvados_cwl.done.logtail")
+ @mock.patch("arvados_cwl.get_current_container")
@mock.patch("arvados.collection.CollectionReader")
@mock.patch("arvados.collection.Collection")
- def test_child_failure(self, col, reader, logtail):
+ def test_child_failure(self, col, reader, gcc_mock):
api = mock.MagicMock()
+ api._rootDesc = copy.deepcopy(get_rootDesc())
+ del api._rootDesc.get('resources')['jobs']['methods']['create']
+
+ # Set up runner with mocked runtime_status_update()
+ self.assertFalse(gcc_mock.called)
+ runtime_status_update = mock.MagicMock()
+ arvados_cwl.ArvCwlRunner.runtime_status_update = runtime_status_update
+ runner = arvados_cwl.ArvCwlRunner(api)
+ self.assertEqual(runner.work_api, 'containers')
+
+ # Make sure ArvCwlRunner thinks it's running inside a container so it
+ # adds the logging handler that will call runtime_status_update() mock
+ gcc_mock.return_value = {"uuid" : "zzzzz-dz642-zzzzzzzzzzzzzzz"}
+ self.assertTrue(gcc_mock.called)
+ root_logger = logging.getLogger('')
+ self.assertEqual(1, len(root_logger.handlers))
+ handler = root_logger.handlers[0]
+ self.assertEqual(arvados_cwl.RuntimeStatusLoggingHandler, handler.__class__)
- runner = mock.MagicMock()
- runner.api = api
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.num_retries = 0
runner.ignore_docker_for_reuse = False
runner.intermediate_output_ttl = 0
runner.secret_store = cwltool.secrets.SecretStore()
+ runner.label = mock.MagicMock()
runner.label.return_value = '[container testjob]'
runner.api.containers().get().execute.return_value = {
@@ -517,7 +536,6 @@ class TestContainer(unittest.TestCase):
}
col().open.return_value = []
- logtail.return_value = 'some error detail'
arvjob = arvados_cwl.ArvadosContainer(runner,
mock.MagicMock(),
@@ -542,10 +560,10 @@ class TestContainer(unittest.TestCase):
"modified_at": "2017-05-26T12:01:22Z"
})
- runner.runtime_status_update.assert_called_with(
+ runtime_status_update.assert_called_with(
'error',
- '[container testjob] zzzzz-xvhdp-zzzzzzzzzzzzzzz failed',
- 'some error detail'
+ 'arvados.cwl-runner: [container testjob] (zzzzz-xvhdp-zzzzzzzzzzzzzzz) error log:',
+ ' ** log is empty **'
)
arvjob.output_callback.assert_called_with({"out": "stuff"}, "permanentFail")
commit 8674cfd50ad24171de7d157813819f3383c3353b
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date: Wed Sep 12 15:41:42 2018 -0300
13773: Removed superfluous documentation
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>
diff --git a/doc/api/methods/containers.html.textile.liquid b/doc/api/methods/containers.html.textile.liquid
index f13bf400a..9ebd91d2b 100644
--- a/doc/api/methods/containers.html.textile.liquid
+++ b/doc/api/methods/containers.html.textile.liquid
@@ -83,7 +83,6 @@ table(table table-bordered table-condensed).
|activity|string|A message for the end user about what state the container is currently in.|Optional.|
|errorDetails|string|Additional structured error details.|Optional.|
|warningDetails|string|Additional structured warning details.|Optional.|
-|activityDetails|string|Additional structured activity details.|Optional.|
h2(#scheduling_parameters). {% include 'container_scheduling_parameters' %}
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