[ARVADOS] updated: 281cf5782f0e05133abbd7c66db729bcc52b08e4
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git at public.curoverse.com
Wed Jul 12 17:42:26 EDT 2017
Summary of changes:
sdk/cwl/arvados_cwl/__init__.py | 4 ++--
sdk/cwl/tests/test_job.py | 2 +-
sdk/cwl/tests/test_submit.py | 20 ++++++++++----------
3 files changed, 13 insertions(+), 13 deletions(-)
via 281cf5782f0e05133abbd7c66db729bcc52b08e4 (commit)
via 48cfc124afff473d58bcef61ec056f18eeaf06c9 (commit)
from b4b2bf5948c049d28a65629555e6fed4220608dc (commit)
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commit 281cf5782f0e05133abbd7c66db729bcc52b08e4
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Jul 12 17:41:32 2017 -0400
Revert "Merge branch '11857-acr-default-crunch2'" (edf37e92f885ed4d5bcf587317cc9c6d90d8ece1)
refs #11857
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curoverse.com>
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 19ebf7f..52009da 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -89,7 +89,7 @@ class ArvCwlRunner(object):
self.collection_cache = CollectionCache(self.api, self.keep_client, self.num_retries)
self.work_api = None
- expected_api = ["containers", "jobs"]
+ expected_api = ["jobs", "containers"]
for api in expected_api:
try:
methods = self.api._rootDesc.get('resources')[api]['methods']
diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index 89f4677..5d140ba 100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -315,7 +315,7 @@ class TestWorkflow(unittest.TestCase):
api._rootDesc = get_rootDesc()
runner = arvados_cwl.ArvCwlRunner(api)
- runner.work_api = 'jobs'
+ self.assertEqual(runner.work_api, 'jobs')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index eec37ef..15cdc1e 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -319,7 +319,7 @@ class TestSubmit(unittest.TestCase):
def test_submit_runner_ram(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-ram=2048",
+ ["--submit", "--no-wait", "--debug", "--submit-runner-ram=2048",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
@@ -338,7 +338,7 @@ class TestSubmit(unittest.TestCase):
def test_submit_invalid_runner_ram(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-ram=-2048",
+ ["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 1)
@@ -350,7 +350,7 @@ class TestSubmit(unittest.TestCase):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--output-name", output_name,
+ ["--submit", "--no-wait", "--debug", "--output-name", output_name,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
@@ -369,7 +369,7 @@ class TestSubmit(unittest.TestCase):
def test_submit_pipeline_name(self, stubs, tm):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--name=hello job 123",
+ ["--submit", "--no-wait", "--debug", "--name=hello job 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
@@ -389,7 +389,7 @@ class TestSubmit(unittest.TestCase):
capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--output-tags", output_tags,
+ ["--submit", "--no-wait", "--debug", "--output-tags", output_tags,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
@@ -408,7 +408,7 @@ class TestSubmit(unittest.TestCase):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs",
+ ["--submit", "--no-wait",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
sys.stdout, sys.stderr, api_client=stubs.api)
@@ -424,7 +424,7 @@ class TestSubmit(unittest.TestCase):
capture_stdout = cStringIO.StringIO()
try:
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--debug",
+ ["--submit", "--no-wait", "--api=containers", "--debug",
"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)
@@ -895,7 +895,7 @@ class TestSubmit(unittest.TestCase):
arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
class TestCreateTemplate(unittest.TestCase):
- existing_template_uuid = "zzzzz-p5p6p-validworkfloyml"
+ existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
def _adjust_script_params(self, expect_component):
expect_component['script_parameters']['x'] = {
@@ -1237,7 +1237,7 @@ class TestTemplateInputs(unittest.TestCase):
@stubs
def test_inputs_empty(self, stubs):
exited = arvados_cwl.main(
- ["--create-template", "--api=jobs",
+ ["--create-template",
"tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
@@ -1248,7 +1248,7 @@ class TestTemplateInputs(unittest.TestCase):
@stubs
def test_inputs(self, stubs):
exited = arvados_cwl.main(
- ["--create-template", "--api=jobs",
+ ["--create-template",
"tests/wf/inputs_test.cwl", "tests/order/inputs_test_order.json"],
cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
commit 48cfc124afff473d58bcef61ec056f18eeaf06c9
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Jul 12 17:39:47 2017 -0400
Revert "11965: Update help message to match new --api default."
refs #11965
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curoverse.com>
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index d642cbd..19ebf7f 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -632,7 +632,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
parser.add_argument("--api", type=str,
default=None, dest="work_api",
choices=("jobs", "containers"),
- help="Select work submission API. Default is 'containers' if that API is available, otherwise 'jobs'.")
+ help="Select work submission API. Default is 'jobs' if that API is available, otherwise 'containers'.")
parser.add_argument("--compute-checksum", action="store_true", default=False,
help="Compute checksum of contents while collecting outputs",
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