#
# SPDX-License-Identifier: Apache-2.0
+from future import standard_library
+standard_library.install_aliases()
+from builtins import object
+from builtins import str
+from future.utils import viewvalues
+
import copy
-import cStringIO
+import io
import functools
import hashlib
import json
import sys
import unittest
+from io import BytesIO
+
+# StringIO.StringIO and io.StringIO have different behavior write() is
+# called with both python2 (byte) strings and unicode strings
+# (specifically there's some logging in cwltool that causes trouble).
+# This isn't a problem on python3 because all string are unicode.
+if sys.version_info[0] < 3:
+ from StringIO import StringIO
+else:
+ from io import StringIO
+
import arvados
import arvados.collection
import arvados_cwl
@mock.patch("arvados.keep.KeepClient")
@mock.patch("arvados.events.subscribe")
def wrapped(self, events, keep_client1, keep_client2, keepdocker, *args, **kwargs):
- class Stubs:
+ class Stubs(object):
pass
stubs = Stubs()
stubs.events = events
stubs.fake_user_uuid = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
stubs.fake_container_uuid = "zzzzz-dz642-zzzzzzzzzzzzzzz"
+ if sys.version_info[0] < 3:
+ stubs.capture_stdout = BytesIO()
+ else:
+ stubs.capture_stdout = StringIO()
+
stubs.api = mock.MagicMock()
stubs.api._rootDesc = get_rootDesc()
+ stubs.api._rootDesc["uuidPrefix"] = "zzzzz"
stubs.api.users().current().execute.return_value = {
"uuid": stubs.fake_user_uuid,
return self.exe
def collection_createstub(created_collections, body, ensure_unique_name=None):
- mt = body["manifest_text"]
+ mt = body["manifest_text"].encode('utf-8')
uuid = "zzzzz-4zz18-zzzzzzzzzzzzzx%d" % len(created_collections)
pdh = "%s+%i" % (hashlib.md5(mt).hexdigest(), len(mt))
created_collections[uuid] = {
"uuid": uuid,
"portable_data_hash": pdh,
- "manifest_text": mt
+ "manifest_text": mt.decode('utf-8')
}
return CollectionExecute(created_collections[uuid])
def collection_getstub(created_collections, uuid):
- for v in created_collections.itervalues():
+ for v in viewvalues(created_collections):
if uuid in (v["uuid"], v["portable_data_hash"]):
return CollectionExecute(v)
"portable_data_hash": "99999999999999999999999999999998+99",
"manifest_text": ". 99999999999999999999999999999998+99 0:0:file1.txt"
},
+ "99999999999999999999999999999997+99": {
+ "uuid": "",
+ "portable_data_hash": "99999999999999999999999999999997+99",
+ "manifest_text": ". 99999999999999999999999999999997+99 0:0:file1.txt"
+ },
"99999999999999999999999999999994+99": {
"uuid": "",
"portable_data_hash": "99999999999999999999999999999994+99",
return '999999999999999999999999999999d4+99'
arvdock.side_effect = get_image
- capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=jobs", "--debug",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
stubs.api.collections().create.assert_has_calls([
mock.call(body=JsonDiffMatcher({
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@mock.patch("time.sleep")
@stubs
def test_submit_no_reuse(self, stubs, tm):
- capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=jobs", "--debug", "--disable-reuse",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:enable_reuse"] = {"value": False}
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_error_when_multiple_storage_classes_specified(self, stubs):
@mock.patch("time.sleep")
@stubs
def test_submit_on_error(self, stubs, tm):
- capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=jobs", "--debug", "--on-error=stop",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:on_error"] = "stop"
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@mock.patch("time.sleep")
@stubs
def test_submit_runner_ram(self, stubs, tm):
- capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--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)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["components"]["cwl-runner"]["runtime_constraints"]["min_ram_mb_per_node"] = 2048
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@mock.patch("time.sleep")
@stubs
def test_submit_invalid_runner_ram(self, stubs, tm):
- capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--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)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 1)
@mock.patch("time.sleep")
def test_submit_output_name(self, stubs, tm):
output_name = "test_output_name"
- capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--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)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["components"]["cwl-runner"]["script_parameters"]["arv:output_name"] = output_name
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@mock.patch("time.sleep")
@stubs
def test_submit_pipeline_name(self, stubs, tm):
- capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--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)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
@mock.patch("time.sleep")
def test_submit_output_tags(self, stubs, tm):
output_tags = "tag0,tag1,tag2"
- capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--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)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
@mock.patch("time.sleep")
@stubs
def test_submit_container(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--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)
- except:
- logging.exception("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
stubs.api.collections().create.assert_has_calls([
mock.call(body=JsonDiffMatcher({
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_no_reuse(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = [
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_reuse_disabled_by_workflow(self, stubs):
- capture_stdout = cStringIO.StringIO()
-
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"tests/wf/submit_wf_no_reuse.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 0)
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
@stubs
def test_submit_container_on_error(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_output_name(self, stubs):
output_name = "test_output_name"
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--output-name", output_name,
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_storage_classes(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
- "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("")
+ exited = arvados_cwl.main(
+ ["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@mock.patch("arvados_cwl.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
return []
job.side_effect = set_final_output
- try:
- exited = arvados_cwl.main(
- ["--debug", "--local", "--storage-classes=foo",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- self.assertEqual(exited, 0)
- except:
- logging.exception("")
+ exited = arvados_cwl.main(
+ ["--debug", "--local", "--storage-classes=foo",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+ self.assertEqual(exited, 0)
@mock.patch("arvados_cwl.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
return []
job.side_effect = set_final_output
- try:
- exited = arvados_cwl.main(
- ["--debug", "--local",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- self.assertEqual(exited, 0)
- except:
- logging.exception("")
+ exited = arvados_cwl.main(
+ ["--debug", "--local",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ sys.stdin, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', 'zzzzz-4zz18-zzzzzzzzzzzzzzzz')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_output_ttl(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_trash_intermediate(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_output_tags(self, stubs):
output_tags = "tag0,tag1,tag2"
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--output-tags", output_tags,
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_runner_ram(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@mock.patch("arvados.collection.CollectionReader")
@mock.patch("time.sleep")
@stubs
def test_submit_file_keepref(self, stubs, tm, collectionReader):
- capture_stdout = cStringIO.StringIO()
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"tests/wf/submit_keepref_wf.cwl"],
- capture_stdout, sys.stderr, api_client=stubs.api)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
-
@mock.patch("arvados.collection.CollectionReader")
@mock.patch("time.sleep")
@stubs
def test_submit_keepref(self, stubs, tm, reader):
- capture_stdout = cStringIO.StringIO()
-
with open("tests/wf/expect_arvworkflow.cwl") as f:
reader().open().__enter__().read.return_value = f.read()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
expect_container = {
'priority': 500,
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@mock.patch("arvados.collection.CollectionReader")
@mock.patch("time.sleep")
@stubs
def test_submit_jobs_keepref(self, stubs, tm, reader):
- capture_stdout = cStringIO.StringIO()
-
with open("tests/wf/expect_arvworkflow.cwl") as f:
reader().open().__enter__().read.return_value = f.read()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=jobs", "--debug",
"keep:99999999999999999999999999999994+99/expect_arvworkflow.cwl#main", "-x", "XxX"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
expect_pipeline["components"]["cwl-runner"]["script_parameters"]["x"] = "XxX"
expect_pipeline["name"] = "expect_arvworkflow.cwl#main"
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
+ self.assertEqual(exited, 0)
@mock.patch("time.sleep")
@stubs
def test_submit_arvworkflow(self, stubs, tm):
- capture_stdout = cStringIO.StringIO()
-
with open("tests/wf/expect_arvworkflow.cwl") as f:
stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
expect_container = {
'priority': 500,
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_name(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["name"] = "hello container 123"
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_submit_missing_input(self, stubs):
- capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--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)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 0)
- capture_stdout = cStringIO.StringIO()
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"tests/wf/submit_wf.cwl", "tests/submit_test_job_missing.json"],
- capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 1)
-
@stubs
def test_submit_container_project(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--project-uuid="+project_uuid,
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["owner_uuid"] = project_uuid
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_eval_timeout(self, stubs):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_collection_cache(self, stubs):
- project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["command"] = ['arvados-cwl-runner', '--local', '--api=containers',
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_submit_job_runner_image(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=jobs", "--debug", "--submit-runner-image=arvados/jobs:123",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
stubs.expect_pipeline_instance["components"]["cwl-runner"]["runtime_constraints"]["docker_image"] = "999999999999999999999999999999d5+99"
expect_pipeline = copy.deepcopy(stubs.expect_pipeline_instance)
stubs.api.pipeline_instances().create.assert_called_with(
body=JsonDiffMatcher(expect_pipeline))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_pipeline_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_runner_image(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99"
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_priority(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
stubs.expect_container_spec["priority"] = 669
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_submit_wf_runner_resources(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug",
- "tests/wf/submit_wf_runner_resources.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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf_runner_resources.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["runtime_constraints"] = {
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
def tearDown(self):
arvados_cwl.arvdocker.arv_docker_clear_cache()
@stubs
def test_submit_secrets(self, stubs):
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug",
- "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
- capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- self.assertEqual(exited, 0)
- except:
- logging.exception("")
-
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = {
"command": [
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_request_uuid(self, stubs):
"state": "Queued"
}
- capture_stdout = cStringIO.StringIO()
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
- "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("")
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-request-uuid=zzzzz-xvhdp-yyyyyyyyyyyyyyy",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
stubs.api.container_requests().update.assert_called_with(
- uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec), cluster_id="zzzzz")
- self.assertEqual(capture_stdout.getvalue(),
+ uuid="zzzzz-xvhdp-yyyyyyyyyyyyyyy", body=JsonDiffMatcher(stubs.expect_container_spec))
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_submit_container_cluster_id(self, stubs):
- capture_stdout = cStringIO.StringIO()
stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
- try:
- exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb",
- "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("")
+
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zbbbb",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container), cluster_id="zbbbb")
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_submit_validate_cluster_id(self, stubs):
- capture_stdout = cStringIO.StringIO()
stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-cluster=zcccc",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 1)
+ @mock.patch("arvados.collection.CollectionReader")
+ @stubs
+ def test_submit_uuid_inputs(self, stubs, collectionReader):
+ collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
+ def list_side_effect(**kwargs):
+ m = mock.MagicMock()
+ if "count" in kwargs:
+ m.execute.return_value = {"items": [
+ {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999998+99"}
+ ]}
+ else:
+ m.execute.return_value = {"items": []}
+ return m
+ stubs.api.collections().list.side_effect = list_side_effect
+
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ expect_container = copy.deepcopy(stubs.expect_container_spec)
+ expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['basename'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
+ expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['y']['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
+ expect_container['mounts']['/var/lib/cwl/cwl.input.json']['content']['z']['listing'][0]['http://arvados.org/cwl#collectionUUID'] = 'zzzzz-4zz18-zzzzzzzzzzzzzzz'
+
+ stubs.api.collections().list.assert_has_calls([
+ mock.call(count='none',
+ filters=[['uuid', 'in', ['zzzzz-4zz18-zzzzzzzzzzzzzzz']]],
+ select=['uuid', 'portable_data_hash'])])
+ stubs.api.container_requests().create.assert_called_with(
+ body=JsonDiffMatcher(expect_container))
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+ @stubs
+ def test_submit_mismatched_uuid_inputs(self, stubs):
+ def list_side_effect(**kwargs):
+ m = mock.MagicMock()
+ if "count" in kwargs:
+ m.execute.return_value = {"items": [
+ {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz", "portable_data_hash": "99999999999999999999999999999997+99"}
+ ]}
+ else:
+ m.execute.return_value = {"items": []}
+ return m
+ stubs.api.collections().list.side_effect = list_side_effect
+
+ for infile in ("tests/submit_test_job_with_mismatched_uuids.json", "tests/submit_test_job_with_inconsistent_uuids.json"):
+ capture_stderr = StringIO()
+ cwltool_logger = logging.getLogger('cwltool')
+ stderr_logger = logging.StreamHandler(capture_stderr)
+ cwltool_logger.addHandler(stderr_logger)
+
+ try:
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf.cwl", infile],
+ stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ self.assertEqual(exited, 1)
+ self.assertRegexpMatches(
+ capture_stderr.getvalue(),
+ r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99")
+ finally:
+ cwltool_logger.removeHandler(stderr_logger)
+
+ @mock.patch("arvados.collection.CollectionReader")
+ @stubs
+ def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
+ collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
+ capture_stderr = StringIO()
+
+ cwltool_logger = logging.getLogger('cwltool')
+ stderr_logger = logging.StreamHandler(capture_stderr)
+ cwltool_logger.addHandler(stderr_logger)
+
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job_with_uuids.json"],
+ stubs.capture_stdout, capture_stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+
+ try:
+ self.assertEqual(exited, 1)
+ self.assertRegexpMatches(
+ capture_stderr.getvalue(),
+ r"Collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz not found")
+ finally:
+ cwltool_logger.removeHandler(stderr_logger)
+
class TestCreateTemplate(unittest.TestCase):
existing_template_uuid = "zzzzz-d1hrv-validworkfloyml"
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
- capture_stdout = cStringIO.StringIO()
-
exited = arvados_cwl.main(
["--create-workflow", "--debug",
"--api=jobs",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
stubs.api.pipeline_instances().create.refute_called()
stubs.api.jobs().create.refute_called()
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_pipeline_template_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_create_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
- capture_stdout = cStringIO.StringIO()
-
exited = arvados_cwl.main(
["--create-workflow", "--debug",
"--project-uuid", project_uuid,
"--api=jobs",
"--name", "testing 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
stubs.api.pipeline_instances().create.refute_called()
stubs.api.jobs().create.refute_called()
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_pipeline_template_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_update_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
- capture_stdout = cStringIO.StringIO()
-
exited = arvados_cwl.main(
["--update-workflow", self.existing_template_uuid,
"--debug",
"--api=jobs",
"--name", "testing 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
stubs.api.pipeline_instances().create.refute_called()
stubs.api.jobs().create.refute_called()
stubs.api.pipeline_templates().update.assert_called_with(
body=JsonDiffMatcher(expect_template), uuid=self.existing_template_uuid)
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
self.existing_template_uuid + '\n')
+ self.assertEqual(exited, 0)
class TestCreateWorkflow(unittest.TestCase):
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
- capture_stdout = cStringIO.StringIO()
-
exited = arvados_cwl.main(
["--create-workflow", "--debug",
"--api=containers",
"--project-uuid", project_uuid,
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
stubs.api.pipeline_templates().create.refute_called()
stubs.api.container_requests().create.refute_called()
stubs.api.workflows().create.assert_called_with(
body=JsonDiffMatcher(body))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_workflow_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_create_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
- capture_stdout = cStringIO.StringIO()
-
exited = arvados_cwl.main(
["--create-workflow", "--debug",
"--api=containers",
"--project-uuid", project_uuid,
"--name", "testing 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
stubs.api.pipeline_templates().create.refute_called()
stubs.api.container_requests().create.refute_called()
stubs.api.workflows().create.assert_called_with(
body=JsonDiffMatcher(body))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_workflow_uuid + '\n')
+ self.assertEqual(exited, 0)
@stubs
def test_incompatible_api(self, stubs):
- capture_stderr = cStringIO.StringIO()
- logging.getLogger('arvados.cwl-runner').addHandler(
- logging.StreamHandler(capture_stderr))
+ capture_stderr = StringIO()
+ acr_logger = logging.getLogger('arvados.cwl-runner')
+ stderr_logger = logging.StreamHandler(capture_stderr)
+ acr_logger.addHandler(stderr_logger)
- exited = arvados_cwl.main(
- ["--update-workflow", self.existing_workflow_uuid,
- "--api=jobs",
- "--debug",
- "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- sys.stderr, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 1)
- self.assertRegexpMatches(
- capture_stderr.getvalue(),
- "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
+ try:
+ exited = arvados_cwl.main(
+ ["--update-workflow", self.existing_workflow_uuid,
+ "--api=jobs",
+ "--debug",
+ "tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
+ sys.stderr, sys.stderr, api_client=stubs.api)
+ self.assertEqual(exited, 1)
+ self.assertRegexpMatches(
+ capture_stderr.getvalue(),
+ "--update-workflow arg '{}' uses 'containers' API, but --api='jobs' specified".format(self.existing_workflow_uuid))
+ finally:
+ acr_logger.removeHandler(stderr_logger)
@stubs
def test_update(self, stubs):
- capture_stdout = cStringIO.StringIO()
-
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--debug",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
body = {
"workflow": {
stubs.api.workflows().update.assert_called_with(
uuid=self.existing_workflow_uuid,
body=JsonDiffMatcher(body))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
self.existing_workflow_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_update_name(self, stubs):
- capture_stdout = cStringIO.StringIO()
-
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--debug", "--name", "testing 123",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
body = {
"workflow": {
stubs.api.workflows().update.assert_called_with(
uuid=self.existing_workflow_uuid,
body=JsonDiffMatcher(body))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
self.existing_workflow_uuid + '\n')
-
+ self.assertEqual(exited, 0)
@stubs
def test_create_collection_per_tool(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
- capture_stdout = cStringIO.StringIO()
-
exited = arvados_cwl.main(
["--create-workflow", "--debug",
"--api=containers",
"--project-uuid", project_uuid,
"tests/collection_per_tool/collection_per_tool.cwl"],
- capture_stdout, sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
expect_workflow = StripYAMLComments(open(toolfile).read())
stubs.api.workflows().create.assert_called_with(
body=JsonDiffMatcher(body))
- self.assertEqual(capture_stdout.getvalue(),
+ self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_workflow_uuid + '\n')
+ self.assertEqual(exited, 0)
class TestTemplateInputs(unittest.TestCase):
expect_template = {
exited = arvados_cwl.main(
["--create-template",
"tests/wf/inputs_test.cwl", "tests/order/empty_order.json"],
- cStringIO.StringIO(), sys.stderr, api_client=stubs.api)
- self.assertEqual(exited, 0)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(self.expect_template), ensure_unique_name=True)
+ self.assertEqual(exited, 0)
+
@stubs
def test_inputs(self, stubs):
exited = arvados_cwl.main(
["--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)
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
expect_template = copy.deepcopy(self.expect_template)
params = expect_template[
stubs.api.pipeline_templates().create.assert_called_with(
body=JsonDiffMatcher(expect_template), ensure_unique_name=True)
+ self.assertEqual(exited, 0)
projects / arvados.git / blobdiff