[ARVADOS] updated: 1.3.0-1466-ga8aa509cf
Git user
git at public.curoverse.com
Thu Aug 8 20:51:04 UTC 2019
Summary of changes:
sdk/cli/test/test_arv-run-pipeline-instance.rb | 37 -------
sdk/cli/test/test_crunch-job.rb | 141 -------------------------
sdk/cwl/tests/test_container.py | 2 -
sdk/python/arvados/commands/run.py | 2 +
4 files changed, 2 insertions(+), 180 deletions(-)
delete mode 100644 sdk/cli/test/test_arv-run-pipeline-instance.rb
delete mode 100644 sdk/cli/test/test_crunch-job.rb
via a8aa509cf3913c8dc91640ddcad6b25e6609517a (commit)
from b96728249db70975be33bb5c5721ec5b8a0eb3ff (commit)
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commit a8aa509cf3913c8dc91640ddcad6b25e6609517a
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Thu Aug 8 16:50:51 2019 -0400
15133: Fix more tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cli/test/test_arv-run-pipeline-instance.rb b/sdk/cli/test/test_arv-run-pipeline-instance.rb
deleted file mode 100644
index b6a0328ad..000000000
--- a/sdk/cli/test/test_arv-run-pipeline-instance.rb
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-require 'minitest/autorun'
-
-class TestRunPipelineInstance < Minitest::Test
- def setup
- end
-
- def test_run_pipeline_instance_get_help
- out, err = capture_subprocess_io do
- system ('arv-run-pipeline-instance -h')
- end
- assert_equal '', err
- end
-
- def test_run_pipeline_instance_with_no_such_option
- out, err = capture_subprocess_io do
- system ('arv-run-pipeline-instance --junk')
- end
- refute_equal '', err
- end
-
- def test_run_pipeline_instance_for_bogus_template_uuid
- out, err = capture_subprocess_io do
- # fails with error SSL_connect error because HOST_INSECURE is not being used
- # system ('arv-run-pipeline-instance --template bogus-abcde-fghijklmnopqrs input=c1bad4b39ca5a924e481008009d94e32+210')
-
- # fails with error: fatal: cannot load such file -- arvados
- # system ('./bin/arv-run-pipeline-instance --template bogus-abcde-fghijklmnopqrs input=c1bad4b39ca5a924e481008009d94e32+210')
- end
- #refute_equal '', err
- assert_equal '', err
- end
-
-end
diff --git a/sdk/cli/test/test_crunch-job.rb b/sdk/cli/test/test_crunch-job.rb
deleted file mode 100644
index 5f111e78d..000000000
--- a/sdk/cli/test/test_crunch-job.rb
+++ /dev/null
@@ -1,141 +0,0 @@
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-require 'minitest/autorun'
-
-class TestCrunchJob < Minitest::Test
- SPECIAL_EXIT = {
- EX_RETRY_UNLOCKED: 93,
- EX_TEMPFAIL: 75,
- }
-
- JOBSPEC = {
- grep_local: {
- owner_uuid: 'zzzzz-j7d0g-it30l961gq3t0oi',
- script: 'grep',
- script_version: 'master',
- repository: File.absolute_path('../../../..', __FILE__),
- script_parameters: {foo: 'bar'},
- },
- }
-
- def setup
- end
-
- def crunchjob
- File.absolute_path '../../bin/crunch-job', __FILE__
- end
-
- # Return environment suitable for running crunch-job.
- def crunchenv opts={}
- env = ENV.to_h
- env['CRUNCH_REFRESH_TRIGGER'] =
- File.absolute_path('../../../../tmp/crunch-refresh-trigger', __FILE__)
- env
- end
-
- def jobspec label
- JOBSPEC[label].dup
- end
-
- # Encode job record to json and run it with crunch-job.
- #
- # opts[:binstubs] is an array of X where ./binstub_X is added to
- # PATH in order to mock system programs.
- def tryjobrecord jobrecord, opts={}
- env = crunchenv
- (opts[:binstubs] || []).each do |binstub|
- env['PATH'] = File.absolute_path('../binstub_'+binstub, __FILE__) + ':' + env['PATH']
- end
- system env, crunchjob, '--job', jobrecord.to_json
- end
-
- def test_bogus_json
- out, err = capture_subprocess_io do
- system crunchenv, crunchjob, '--job', '"}{"'
- end
- assert_equal false, $?.success?
- # Must not conflict with our special exit statuses
- assert_jobfail $?
- assert_match /JSON/, err
- end
-
- def test_fail_sanity_check
- out, err = capture_subprocess_io do
- j = {}
- tryjobrecord j, binstubs: ['sanity_check']
- end
- assert_equal 75, $?.exitstatus
- assert_match /Sanity check failed: 7/, err
- end
-
- def test_fail_docker_sanity_check
- out, err = capture_subprocess_io do
- j = {}
- j[:docker_image_locator] = '4d449b9d34f2e2222747ef79c53fa3ff+1234'
- tryjobrecord j, binstubs: ['sanity_check']
- end
- assert_equal 75, $?.exitstatus
- assert_match /Sanity check failed: 8/, err
- end
-
- def test_no_script_specified
- out, err = capture_subprocess_io do
- j = jobspec :grep_local
- j.delete :script
- tryjobrecord j
- end
- assert_match /No script specified/, err
- assert_jobfail $?
- end
-
- def test_fail_clean_tmp
- out, err = capture_subprocess_io do
- j = jobspec :grep_local
- tryjobrecord j, binstubs: ['clean_fail']
- end
- assert_match /Failing mount stub was called/, err
- assert_match /clean work dirs: exit 44\n.*Transient failure.* exiting 93\n(.*arv_put.*INFO.*\n)?$/, err
- assert_equal SPECIAL_EXIT[:EX_RETRY_UNLOCKED], $?.exitstatus
- end
-
- def test_output_collection_owner_uuid
- skip "Depends on a post 1.3 python-arvados-python-client package being installed"
-
- j = jobspec :grep_local
- out, err = capture_subprocess_io do
- tryjobrecord j, binstubs: ['arv-mount', 'output_coll_owner']
- end
- assert_match /owner_uuid: #{j['owner_uuid']}/, err
- end
-
- def test_docker_image_missing
- skip 'API bug: it refuses to create this job in Running state'
- out, err = capture_subprocess_io do
- j = jobspec :grep_local
- j[:docker_image_locator] = '4d449b9d34f2e2222747ef79c53fa3ff+1234'
- tryjobrecord j, binstubs: ['docker_noop']
- end
- assert_match /No Docker image hash found from locator/, err
- assert_jobfail $?
- end
-
- def test_script_version_not_found_in_repository
- bogus_version = 'f8b72707c1f5f740dbf1ed56eb429a36e0dee770'
- out, err = capture_subprocess_io do
- j = jobspec :grep_local
- j[:script_version] = bogus_version
- tryjobrecord j, binstubs: ['arv-mount']
- end
- assert_match /'#{bogus_version}' not found, giving up/, err
- assert_jobfail $?
- end
-
- # Ensure procstatus is not interpreted as a temporary infrastructure
- # problem. Would be assert_http_4xx if this were http.
- def assert_jobfail procstatus
- refute_includes SPECIAL_EXIT.values, procstatus.exitstatus
- assert_equal false, procstatus.success?
- end
-end
diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index c22ece38b..3374e1c13 100644
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -88,7 +88,6 @@ class TestContainer(unittest.TestCase):
def setup_and_test_container_executor_and_logging(self, gcc_mock) :
api = mock.MagicMock()
api._rootDesc = copy.deepcopy(get_rootDesc())
- del api._rootDesc.get('resources')['jobs']['methods']['create']
# Make sure ArvCwlExecutor thinks it's running inside a container so it
# adds the logging handler that will call runtime_status_update() mock
@@ -1071,6 +1070,5 @@ class TestWorkflow(unittest.TestCase):
api = mock.MagicMock()
api._rootDesc = copy.deepcopy(get_rootDesc())
- del api._rootDesc.get('resources')['jobs']['methods']['create']
runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'containers')
diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index f0d518d4e..a45775470 100644
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -39,6 +39,8 @@ import arvados.config as config
from arvados._version import __version__
+logger = logging.getLogger('arvados.arv-run')
+logger.setLevel(logging.INFO)
class ArvFile(object):
def __init__(self, prefix, fn):
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