[ARVADOS] updated: 1.1.3-345-g091c2bc
Git user
git at public.curoverse.com
Fri Apr 6 13:37:18 EDT 2018
Summary of changes:
sdk/cwl/tests/test_submit.py | 76 ++++++++++++++++++++++++++++++++++----------
1 file changed, 60 insertions(+), 16 deletions(-)
via 091c2bc58ff1a8d1c43abf0e334837d8872b914d (commit)
from 6aef698e8f1f99aa0511afd21db86d4c7cf8b5da (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 091c2bc58ff1a8d1c43abf0e334837d8872b914d
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Fri Apr 6 13:37:08 2018 -0400
13108: Fix tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index a7f4920..77bef07 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -168,6 +168,7 @@ def stubs(func):
}
]}},
'cwl:tool': '3fffdeaa75e018172e1b583425f4ebff+60/workflow.cwl#main',
+ 'arv:debug': True,
'arv:enable_reuse': True,
'arv:on_error': 'continue'
},
@@ -236,7 +237,8 @@ def stubs(func):
'owner_uuid': None,
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'name': 'submit_wf.cwl',
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
@@ -444,7 +446,7 @@ class TestSubmit(unittest.TestCase):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
exited = arvados_cwl.main(
- ["--submit", "--no-wait",
+ ["--submit", "--no-wait", "--debug",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
sys.stdout, sys.stderr, api_client=stubs.api)
@@ -503,7 +505,8 @@ class TestSubmit(unittest.TestCase):
expect_container["command"] = [
'arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--disable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--eval-timeout=20', '--thread-count=4',
+ '--disable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["use_existing"] = False
@@ -527,7 +530,8 @@ class TestSubmit(unittest.TestCase):
expect_container["command"] = [
'arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--disable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--eval-timeout=20', '--thread-count=4',
+ '--disable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["use_existing"] = False
expect_container["name"] = "submit_wf_no_reuse.cwl"
@@ -563,7 +567,8 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=stop', '--eval-timeout=20',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=stop',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
@@ -588,7 +593,9 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- "--output-name="+output_name, '--enable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse',
+ "--output-name="+output_name, '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["output_name"] = output_name
@@ -613,8 +620,9 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue',
- "--intermediate-output-ttl=3600", '--eval-timeout=20',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
+ "--intermediate-output-ttl=3600",
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
@@ -637,8 +645,9 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue',
- "--trash-intermediate", '--eval-timeout=20',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
+ "--trash-intermediate",
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
@@ -663,7 +672,9 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- "--output-tags="+output_tags, '--enable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse',
+ "--output-tags="+output_tags, '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
@@ -746,7 +757,8 @@ class TestSubmit(unittest.TestCase):
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow/expect_arvworkflow.cwl#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
@@ -864,7 +876,8 @@ class TestSubmit(unittest.TestCase):
'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue', '--eval-timeout=20',
+ '--eval-timeout=20', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
'cwd': '/var/spool/cwl',
'runtime_constraints': {
@@ -923,7 +936,9 @@ class TestSubmit(unittest.TestCase):
expect_container["owner_uuid"] = project_uuid
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue', '--project-uuid='+project_uuid, '--eval-timeout=20',
+ "--eval-timeout=20", "--thread-count=4",
+ '--enable-reuse', '--debug', '--on-error=continue',
+ '--project-uuid='+project_uuid,
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
@@ -947,7 +962,34 @@ class TestSubmit(unittest.TestCase):
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate',
- '--enable-reuse', '--on-error=continue', '--eval-timeout=60.0',
+ '--eval-timeout=60.0', '--thread-count=4',
+ '--enable-reuse', '--debug', '--on-error=continue',
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+
+
+ @stubs
+ def test_submit_container_thread_count(self, stubs):
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ capture_stdout = cStringIO.StringIO()
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ self.assertEqual(exited, 0)
+ except:
+ logging.exception("")
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
+ '--no-log-timestamps', '--disable-validate',
+ '--eval-timeout=20', '--thread-count=20',
+ '--enable-reuse', '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
@@ -1069,9 +1111,11 @@ class TestSubmit(unittest.TestCase):
"--api=containers",
"--no-log-timestamps",
"--disable-validate",
+ "--eval-timeout=20",
+ '--thread-count=4',
"--enable-reuse",
+ '--debug',
"--on-error=continue",
- "--eval-timeout=20",
"/var/lib/cwl/workflow.json#main",
"/var/lib/cwl/cwl.input.json"
],
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list