#
# 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 io
+import itertools
import functools
import hashlib
import json
import logging
-import mock
import sys
import unittest
import cwltool.process
import re
+import os
-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
+from io import BytesIO, StringIO
+from unittest import mock
import arvados
import arvados.collection
from .matcher import JsonDiffMatcher, StripYAMLComments
from .mock_discovery import get_rootDesc
-import ruamel.yaml as yaml
+import ruamel.yaml
_rootDesc = None
-def stubs(wfname='submit_wf.cwl'):
+def stubs(wfdetails=('submit_wf.cwl', None)):
def outer_wrapper(func, *rest):
@functools.wraps(func)
@mock.patch("arvados_cwl.arvdocker.determine_image_id")
uuid4, determine_image_id, *args, **kwargs):
class Stubs(object):
pass
+
+ wfname = wfdetails[0]
+ wfpath = wfdetails[1]
+
stubs = Stubs()
stubs.events = events
stubs.keepdocker = keepdocker
uuid4.side_effect = ["df80736f-f14d-4b10-b2e3-03aa27f034bb", "df80736f-f14d-4b10-b2e3-03aa27f034b1",
"df80736f-f14d-4b10-b2e3-03aa27f034b2", "df80736f-f14d-4b10-b2e3-03aa27f034b3",
- "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5"]
+ "df80736f-f14d-4b10-b2e3-03aa27f034b4", "df80736f-f14d-4b10-b2e3-03aa27f034b5",
+ "df80736f-f14d-4b10-b2e3-03aa27f034b6", "df80736f-f14d-4b10-b2e3-03aa27f034b7",
+ "df80736f-f14d-4b10-b2e3-03aa27f034b8", "df80736f-f14d-4b10-b2e3-03aa27f034b9",
+ "df80736f-f14d-4b10-b2e3-03aa27f034c0", "df80736f-f14d-4b10-b2e3-03aa27f034c1",
+ "df80736f-f14d-4b10-b2e3-03aa27f034c2", "df80736f-f14d-4b10-b2e3-03aa27f034c3",
+ "df80736f-f14d-4b10-b2e3-03aa27f034c4", "df80736f-f14d-4b10-b2e3-03aa27f034c5",
+ "df80736f-f14d-4b10-b2e3-03aa27f034c6", "df80736f-f14d-4b10-b2e3-03aa27f034c7"]
determine_image_id.return_value = None
return CollectionExecute(created_collections[uuid])
def collection_getstub(created_collections, uuid):
- for v in viewvalues(created_collections):
+ for v in created_collections.values():
if uuid in (v["uuid"], v["portable_data_hash"]):
return CollectionExecute(v)
stubs.api.collections().create.side_effect = functools.partial(collection_createstub, created_collections)
stubs.api.collections().get.side_effect = functools.partial(collection_getstub, created_collections)
- stubs.expect_job_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
- stubs.api.jobs().create().execute.return_value = {
- "uuid": stubs.expect_job_uuid,
- "state": "Queued",
- }
-
stubs.expect_container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
stubs.api.container_requests().create().execute.return_value = {
"uuid": stubs.expect_container_request_uuid,
"state": "Queued"
}
- stubs.expect_pipeline_template_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
- stubs.api.pipeline_templates().create().execute.return_value = {
- "uuid": stubs.expect_pipeline_template_uuid,
- }
- stubs.expect_job_spec = {
- 'runtime_constraints': {
- 'docker_image': '999999999999999999999999999999d3+99',
- 'min_ram_mb_per_node': 1024
- },
- 'script_parameters': {
- 'x': {
- 'basename': 'blorp.txt',
- 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
- 'class': 'File'
- },
- 'y': {
- 'basename': '99999999999999999999999999999998+99',
- 'location': 'keep:99999999999999999999999999999998+99',
- 'class': 'Directory'
- },
- 'z': {
- 'basename': 'anonymous',
- "listing": [{
- "basename": "renamed.txt",
- "class": "File",
- "location": "keep:99999999999999999999999999999998+99/file1.txt",
- "size": 0
- }],
- 'class': 'Directory'
- },
- 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main'
- },
- 'repository': 'arvados',
- 'script_version': 'master',
- 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
- 'script': 'cwl-runner'
- }
- stubs.pipeline_component = stubs.expect_job_spec.copy()
- stubs.expect_pipeline_instance = {
- 'name': 'submit_wf.cwl',
- 'state': 'RunningOnServer',
- 'owner_uuid': None,
- "components": {
- "cwl-runner": {
- 'runtime_constraints': {'docker_image': '999999999999999999999999999999d3+99', 'min_ram_mb_per_node': 1024},
- 'script_parameters': {
- 'y': {"value": {'basename': '99999999999999999999999999999998+99', 'location': 'keep:99999999999999999999999999999998+99', 'class': 'Directory'}},
- 'x': {"value": {
- 'basename': 'blorp.txt',
- 'class': 'File',
- 'location': 'keep:169f39d466a5438ac4a90e779bf750c7+53/blorp.txt',
- "size": 16
- }},
- 'z': {"value": {'basename': 'anonymous', 'class': 'Directory',
- 'listing': [
- {
- 'basename': 'renamed.txt',
- 'class': 'File', 'location':
- 'keep:99999999999999999999999999999998+99/file1.txt',
- 'size': 0
- }
- ]}},
- 'cwl:tool': '57ad063d64c60dbddc027791f0649211+60/workflow.cwl#main',
- 'arv:debug': True,
- 'arv:enable_reuse': True,
- 'arv:on_error': 'continue'
- },
- 'repository': 'arvados',
- 'script_version': 'master',
- 'minimum_script_version': '570509ab4d2ef93d870fd2b1f2eab178afb1bad9',
- 'script': 'cwl-runner',
- 'job': {'state': 'Queued', 'uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}
- }
- }
- }
- stubs.pipeline_create = copy.deepcopy(stubs.expect_pipeline_instance)
- stubs.expect_pipeline_uuid = "zzzzz-d1hrv-zzzzzzzzzzzzzzz"
- stubs.pipeline_create["uuid"] = stubs.expect_pipeline_uuid
- stubs.pipeline_with_job = copy.deepcopy(stubs.pipeline_create)
- stubs.pipeline_with_job["components"]["cwl-runner"]["job"] = {
- "uuid": "zzzzz-8i9sb-zzzzzzzzzzzzzzz",
- "state": "Queued"
- }
- stubs.api.pipeline_instances().create().execute.return_value = stubs.pipeline_create
- stubs.api.pipeline_instances().get().execute.return_value = stubs.pipeline_with_job
+ cwd = os.getcwd()
+ filepath = os.path.join(cwd, "tests/wf/submit_wf_wrapper.cwl")
+ with open(filepath) as f:
+ yaml = ruamel.yaml.YAML(typ='rt', pure=True)
+ expect_packed_workflow = yaml.load(f)
- with open("tests/wf/submit_wf_packed.cwl") as f:
- expect_packed_workflow = yaml.round_trip_load(f)
+ if wfpath is None:
+ wfpath = wfname
+
+ gitinfo_workflow = copy.deepcopy(expect_packed_workflow)
+ gitinfo_workflow["$graph"][0]["id"] = "file://%s/tests/wf/%s" % (cwd, wfpath)
+ mocktool = mock.NonCallableMock(tool=gitinfo_workflow["$graph"][0], metadata=gitinfo_workflow)
+
+ stubs.git_info = arvados_cwl.executor.ArvCwlExecutor.get_git_info(mocktool)
+ expect_packed_workflow.update(stubs.git_info)
+
+ stubs.git_props = {"arv:"+k.split("#", 1)[1]: v for k,v in stubs.git_info.items()}
+
+ step_name = "%s (%s)" % (wfpath, stubs.git_props["arv:gitDescribe"])
+ if wfname == wfpath:
+ container_name = "%s (%s)" % (wfpath, stubs.git_props["arv:gitDescribe"])
+ else:
+ container_name = wfname
+
+ expect_packed_workflow["$graph"][0]["steps"][0]["id"] = "#main/"+step_name
+ expect_packed_workflow["$graph"][0]["steps"][0]["label"] = container_name
stubs.expect_container_spec = {
'priority': 500,
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- '--output-name=Output from workflow '+wfname,
+ '--output-name=Output from workflow '+container_name,
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
- 'name': wfname,
+ 'name': container_name,
'container_image': '999999999999999999999999999999d3+99',
- 'output_name': 'Output from workflow '+wfname,
+ 'output_name': 'Output from workflow %s' % (container_name),
'output_path': '/var/spool/cwl',
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'vcpus': 1,
'ram': (1024+256)*1024*1024
},
+ 'properties': stubs.git_props,
'use_existing': False,
- 'properties': {},
'secret_mounts': {}
}
def setUp(self):
cwltool.process._names = set()
- arvados_cwl.arvdocker.arv_docker_clear_cache()
+ #arvados_cwl.arvdocker.arv_docker_clear_cache()
def tearDown(self):
root_logger = logging.getLogger('')
root_logger.handlers = handlers
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_invalid_runner_ram(self, stubs, tm):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--debug", "--submit-runner-ram=-2048",
self.assertEqual(exited, 1)
- @stubs
+ @stubs()
def test_submit_container(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
'manifest_text':
'. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
'replication_desired': None,
- 'name': 'submit_wf.cwl input (169f39d466a5438ac4a90e779bf750c7+53)',
+ 'name': 'submit_wf.cwl ('+ stubs.git_props["arv:gitDescribe"] +') input (169f39d466a5438ac4a90e779bf750c7+53)',
}), ensure_unique_name=False),
mock.call(body=JsonDiffMatcher({
'manifest_text':
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_tool(self, stubs):
# test for issue #16139
exited = arvados_cwl.main(
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_no_reuse(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--disable-reuse",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--disable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["use_existing"] = False
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs('submit_wf_no_reuse.cwl')
+ @stubs(('submit_wf_no_reuse.cwl', None))
def test_submit_container_reuse_disabled_by_workflow(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
self.assertEqual(exited, 0)
expect_container = copy.deepcopy(stubs.expect_container_spec)
- expect_container["command"] = [
- 'arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=0',
- '--disable-reuse', "--collection-cache-size=256",
- '--output-name=Output from workflow submit_wf_no_reuse.cwl', '--debug', '--on-error=continue',
- '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+ expect_container["command"] = ["--disable-reuse" if v == "--enable-reuse" else v for v in expect_container["command"]]
expect_container["use_existing"] = False
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [
{
- "class": "http://arvados.org/cwl#ReuseRequirement",
+ "class": "WorkReuse",
"enableReuse": False,
},
+ {
+ "acrContainerImage": "999999999999999999999999999999d3+99",
+ "class": "http://arvados.org/cwl#WorkflowRunnerResources"
+ }
]
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
- "arv": "http://arvados.org/cwl#",
- "cwltool": "http://commonwl.org/cwltool#"
- }
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:fa5fbf21deb74f9f239daa3f5bb4b902+292/wf/submit_wf_no_reuse.cwl"
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
stubs.expect_container_request_uuid + '\n')
- @stubs
+ @stubs()
def test_submit_container_on_error(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--on-error=stop",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=stop',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_output_name(self, stubs):
output_name = "test_output_name"
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_storage_classes(self, stubs):
exited = arvados_cwl.main(
["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- '--output-name=Output from workflow submit_wf.cwl',
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
"--debug",
"--storage-classes=foo", '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_multiple_storage_classes(self, stubs):
exited = arvados_cwl.main(
["--debug", "--submit", "--no-wait", "--api=containers", "--storage-classes=foo,bar", "--intermediate-storage-classes=baz",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
"--debug",
"--storage-classes=foo,bar", "--intermediate-storage-classes=baz", '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
@mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
@mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
- @stubs
+ @stubs()
def test_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
final_output_c = arvados.collection.Collection()
make_output.return_value = ({},final_output_c)
job.side_effect = set_final_output
exited = arvados_cwl.main(
- ["--debug", "--local", "--storage-classes=foo",
+ ["--debug", "--local", "--storage-classes=foo", "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
+ make_output.assert_called_with(u'Output from workflow submit_wf.cwl', ['foo'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
@mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
@mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
- @stubs
+ @stubs()
def test_default_storage_classes_correctly_propagate_to_make_output_collection(self, stubs, make_output, job, tq):
final_output_c = arvados.collection.Collection()
make_output.return_value = ({},final_output_c)
job.side_effect = set_final_output
exited = arvados_cwl.main(
- ["--debug", "--local",
+ ["--debug", "--local", "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
+ make_output.assert_called_with(u'Output from workflow submit_wf.cwl', ['default'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
@mock.patch("cwltool.task_queue.TaskQueue")
@mock.patch("arvados_cwl.arvworkflow.ArvadosWorkflow.job")
@mock.patch("arvados_cwl.executor.ArvCwlExecutor.make_output_collection")
- @stubs
+ @stubs()
def test_storage_class_hint_to_make_output_collection(self, stubs, make_output, job, tq):
final_output_c = arvados.collection.Collection()
make_output.return_value = ({},final_output_c)
job.side_effect = set_final_output
exited = arvados_cwl.main(
- ["--debug", "--local",
+ ["--debug", "--local", "--disable-git",
"tests/wf/submit_storage_class_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
- make_output.assert_called_with(u'Output of submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
+ make_output.assert_called_with(u'Output from workflow submit_storage_class_wf.cwl', ['foo', 'bar'], '', {}, {"out": "zzzzz"})
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_output_ttl(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--intermediate-output-ttl", "3600",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl", '--debug',
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug',
'--on-error=continue',
"--intermediate-output-ttl=3600",
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_trash_intermediate(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--trash-intermediate",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=continue',
"--trash-intermediate",
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_output_tags(self, stubs):
output_tags = "tag0,tag1,tag2"
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
"--output-tags="+output_tags, '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_runner_ram(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-ram=2048",
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container["runtime_constraints"]["ram"] = (2048+256)*1024*1024
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [
+ {
+ "acrContainerImage": "999999999999999999999999999999d3+99",
+ "class": "http://arvados.org/cwl#WorkflowRunnerResources",
+ "ramMin": 2048
+ }
+ ]
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
@mock.patch("arvados.collection.CollectionReader")
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_file_keepref(self, stubs, tm, collectionReader):
collectionReader().exists.return_value = True
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "blorp.txt")
@mock.patch("arvados.collection.CollectionReader")
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_keepref(self, stubs, tm, reader):
with open("tests/wf/expect_arvworkflow.cwl") as f:
reader().open().__enter__().read.return_value = f.read()
self.assertEqual(exited, 0)
@mock.patch("time.sleep")
- @stubs
+ @stubs()
def test_submit_arvworkflow(self, stubs, tm):
with open("tests/wf/expect_arvworkflow.cwl") as f:
stubs.api.workflows().get().execute.return_value = {"definition": f.read(), "name": "a test workflow"}
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug",
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-git",
"962eh-7fd4e-gkbzl62qqtfig37", "-x", "XxX"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
'kind': 'json',
'content': {
'cwlVersion': 'v1.0',
+ 'label': 'a test workflow',
'$graph': [
{
'id': '#main',
'requirements': [
{
'dockerPull': 'debian:buster-slim',
- 'class': 'DockerRequirement',
- "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
+ 'class': 'DockerRequirement'
}
],
'id': '#submit_tool.cwl',
'command': ['arvados-cwl-runner', '--local', '--api=containers',
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--enable-reuse', "--collection-cache-size=256",
+ "--output-name=Output from workflow a test workflow",
+ '--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json'],
+ 'output_name': 'Output from workflow a test workflow',
'cwd': '/var/spool/cwl',
'runtime_constraints': {
'API': True,
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs('hello container 123')
+ @stubs(('hello container 123', 'submit_wf.cwl'))
def test_submit_container_name(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--name=hello container 123",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_missing_input(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 1)
- @stubs
+ @stubs()
def test_submit_container_project(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
'--no-log-timestamps', '--disable-validate', '--disable-color',
"--eval-timeout=20", "--thread-count=0",
'--enable-reuse', "--collection-cache-size=256",
- "--output-name=Output from workflow submit_wf.cwl", '--debug',
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug',
'--on-error=continue',
'--project-uuid='+project_uuid,
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_eval_timeout(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--eval-timeout=60",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=60.0', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_collection_cache(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--collection-cache-size=500",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=0',
'--enable-reuse', "--collection-cache-size=500",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
expect_container["runtime_constraints"]["ram"] = (1024+500)*1024*1024
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_thread_count(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--thread-count=20",
'--no-log-timestamps', '--disable-validate', '--disable-color',
'--eval-timeout=20', '--thread-count=20',
'--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
'--debug', '--on-error=continue',
'/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_runner_image(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--submit-runner-image=arvados/jobs:123",
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
stubs.expect_container_spec["container_image"] = "999999999999999999999999999999d5+99"
+ stubs.expect_container_spec["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [
+ {
+ "acrContainerImage": "999999999999999999999999999999d5+99",
+ "class": "http://arvados.org/cwl#WorkflowRunnerResources"
+ }
+ ]
expect_container = copy.deepcopy(stubs.expect_container_spec)
stubs.api.container_requests().create.assert_called_with(
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_priority(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--priority=669",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs('submit_wf_runner_resources.cwl')
+ @stubs(('submit_wf_runner_resources.cwl', None))
def test_submit_wf_runner_resources(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
"vcpus": 2,
"ram": (2000+512) * 2**20
}
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [
{
"class": "http://arvados.org/cwl#WorkflowRunnerResources",
+ "acrContainerImage": "999999999999999999999999999999d3+99",
"coresMin": 2,
"ramMin": 2000,
"keep_cache": 512
}
]
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
- "arv": "http://arvados.org/cwl#",
- }
- expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=512",
- '--output-name=Output from workflow submit_wf_runner_resources.cwl',
- '--debug', '--on-error=continue',
- '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+ #expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
+ # "arv": "http://arvados.org/cwl#",
+ #}
+ expect_container["command"] = ["--collection-cache-size=512" if v == "--collection-cache-size=256" else v for v in expect_container["command"]]
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:80b60e39456505b91d3989a1f5058b98+308/wf/submit_wf_runner_resources.cwl"
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
@mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
@mock.patch("arvados.api")
def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
- arvados_cwl.arvdocker.arv_docker_clear_cache()
+ #arvados_cwl.arvdocker.arv_docker_clear_cache()
arvrunner = mock.MagicMock()
arvrunner.project_uuid = ""
api.return_value = mock.MagicMock()
arvrunner.api = api.return_value
arvrunner.runtimeContext.match_local_docker = False
- arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
- "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "link_class": "docker_image_repo+tag",
- "name": "arvados/jobs:"+arvados_cwl.__version__,
- "owner_uuid": "",
- "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
- {"items": [{"created_at": "",
- "head_uuid": "",
- "link_class": "docker_image_hash",
- "name": "123456",
- "owner_uuid": "",
- "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
- {"items": [{"created_at": "",
- "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "link_class": "docker_image_repo+tag",
- "name": "arvados/jobs:"+arvados_cwl.__version__,
- "owner_uuid": "",
- "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
- {"items": [{"created_at": "",
- "head_uuid": "",
- "link_class": "docker_image_hash",
- "name": "123456",
- "owner_uuid": "",
- "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
- )
+ arvrunner.api.links().list().execute.side_effect = itertools.cycle([
+ {"items": [{"created_at": "2023-08-25T12:34:56.123456Z",
+ "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+ "link_class": "docker_image_repo+tag",
+ "name": "arvados/jobs:"+arvados_cwl.__version__,
+ "owner_uuid": "",
+ "uuid": "zzzzz-o0j2j-arvadosjobsrepo",
+ "properties": {"image_timestamp": ""}}]},
+ {"items": []},
+ {"items": []},
+ {"items": [{"created_at": "2023-08-25T12:34:57.234567Z",
+ "head_uuid": "",
+ "link_class": "docker_image_hash",
+ "name": "123456",
+ "owner_uuid": "",
+ "uuid": "zzzzz-o0j2j-arvadosjobshash",
+ "properties": {"image_timestamp": ""}}]},
+ {"items": []},
+ {"items": []},
+ ])
find_one_image_hash.return_value = "123456"
- arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "owner_uuid": "",
- "manifest_text": "",
- "properties": ""
- }], "items_available": 1, "offset": 0},
- {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "owner_uuid": "",
- "manifest_text": "",
- "properties": ""
- }], "items_available": 1, "offset": 0})
+ arvrunner.api.collections().list().execute.side_effect = itertools.cycle([
+ {"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+ "owner_uuid": "",
+ "manifest_text": "",
+ "created_at": "2023-08-25T12:34:55.012345Z",
+ "properties": {}}]},
+ {"items": []},
+ {"items": []},
+ ])
arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
"portable_data_hash": "9999999999999999999999999999999b+99"}
arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__, arvrunner.runtimeContext))
- @stubs
+ @stubs()
def test_submit_secrets(self, stubs):
exited = arvados_cwl.main(
- ["--submit", "--no-wait", "--api=containers", "--debug",
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--disable-git",
"tests/wf/secret_wf.cwl", "tests/secret_test_job.yml"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
+ stubs.git_props["arv:gitPath"] = "sdk/cwl/tests/wf/secret_wf.cwl"
+ stubs.git_info["http://arvados.org/cwl#gitPath"] = "sdk/cwl/tests/wf/secret_wf.cwl"
+
expect_container = {
"command": [
"arvados-cwl-runner",
'--thread-count=0',
"--enable-reuse",
"--collection-cache-size=256",
- '--output-name=Output from workflow secret_wf.cwl'
- '--debug',
+ "--output-name=Output from workflow secret_wf.cwl",
+ "--debug",
"--on-error=continue",
"/var/lib/cwl/workflow.json#main",
"/var/lib/cwl/cwl.input.json"
"/var/lib/cwl/workflow.json": {
"content": {
"$graph": [
- {
- "arguments": [
- "md5sum",
- "example.conf"
- ],
- "class": "CommandLineTool",
- "hints": [
- {
- "class": "http://commonwl.org/cwltool#Secrets",
- "secrets": [
- "#secret_job.cwl/pw"
- ]
- }
- ],
- "id": "#secret_job.cwl",
- "inputs": [
- {
- "id": "#secret_job.cwl/pw",
- "type": "string"
- }
- ],
- "outputs": [
- {
- "id": "#secret_job.cwl/out",
- "type": "File",
- "outputBinding": {
- "glob": "hashed_example.txt"
- }
- }
- ],
- "stdout": "hashed_example.txt",
- "requirements": [
- {
- "class": "InitialWorkDirRequirement",
- "listing": [
- {
- "entry": "username: user\npassword: $(inputs.pw)\n",
- "entryname": "example.conf"
- }
- ]
- }
- ]
- },
{
"class": "Workflow",
"hints": [
{
- "class": "DockerRequirement",
- "dockerPull": "debian:buster-slim",
- "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
+ "class": "DockerRequirement",
+ "dockerPull": "debian:buster-slim",
+ "http://arvados.org/cwl#dockerCollectionPDH": "999999999999999999999999999999d4+99"
},
{
"class": "http://commonwl.org/cwltool#Secrets",
"secrets": [
"#main/pw"
]
+ },
+ {
+ "acrContainerImage": "999999999999999999999999999999d3+99",
+ "class": "http://arvados.org/cwl#WorkflowRunnerResources"
}
],
"id": "#main",
"outputs": [
{
"id": "#main/out",
- "outputSource": "#main/step1/out",
+ "outputSource": "#main/step/out",
"type": "File"
}
],
+ "requirements": [
+ {
+ "class": "SubworkflowFeatureRequirement"
+ }
+ ],
"steps": [
{
- "id": "#main/step1",
+ "id": "#main/secret_wf.cwl",
"in": [
{
- "id": "#main/step1/pw",
+ "id": "#main/step/pw",
"source": "#main/pw"
}
],
+ "label": "secret_wf.cwl",
"out": [
- "#main/step1/out"
+ {"id": "#main/step/out"}
],
- "run": "#secret_job.cwl"
+ "run": "keep:991302581d01db470345a131480e623b+247/secret_wf.cwl"
}
]
}
],
- "$namespaces": {
- "cwltool": "http://commonwl.org/cwltool#"
- },
- "cwlVersion": "v1.0"
+ "cwlVersion": "v1.2"
},
"kind": "json"
},
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_request_uuid(self, stubs):
stubs.api._rootDesc["remoteHosts"]["zzzzz"] = "123"
stubs.expect_container_request_uuid = "zzzzz-xvhdp-yyyyyyyyyyyyyyy"
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_container_cluster_id(self, stubs):
stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_validate_cluster_id(self, stubs):
stubs.api._rootDesc["remoteHosts"]["zbbbb"] = "123"
exited = arvados_cwl.main(
stubs.capture_stdout, sys.stderr, api_client=stubs.api, keep_client=stubs.keep_client)
self.assertEqual(exited, 1)
- @stubs
+ @stubs()
def test_submit_validate_project_uuid(self, stubs):
# Fails with bad cluster prefix
exited = arvados_cwl.main(
@mock.patch("arvados.collection.CollectionReader")
- @stubs
+ @stubs()
def test_submit_uuid_inputs(self, stubs, collectionReader):
collectionReader().exists.return_value = True
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
m.execute.return_value = {"items": []}
return m
stubs.api.collections().list.side_effect = list_side_effect
+ collectionReader().portable_data_hash.return_value = "99999999999999999999999999999998+99"
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_mismatched_uuid_inputs(self, stubs):
def list_side_effect(**kwargs):
m = mock.MagicMock()
cwltool_logger.removeHandler(stderr_logger)
@mock.patch("arvados.collection.CollectionReader")
- @stubs
+ @stubs()
def test_submit_unknown_uuid_inputs(self, stubs, collectionReader):
collectionReader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "file1.txt")
capture_stderr = StringIO()
finally:
cwltool_logger.removeHandler(stderr_logger)
- @stubs('submit_wf_process_properties.cwl')
+ @stubs(('submit_wf_process_properties.cwl', None))
def test_submit_set_process_properties(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug",
expect_container = copy.deepcopy(stubs.expect_container_spec)
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][1]["hints"] = [
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["hints"] = [
{
"class": "http://arvados.org/cwl#ProcessProperties",
"processProperties": [
}
}
],
+ },
+ {
+ "acrContainerImage": "999999999999999999999999999999d3+99",
+ "class": "http://arvados.org/cwl#WorkflowRunnerResources"
}
]
- expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
- "arv": "http://arvados.org/cwl#"
- }
+ #expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$namespaces"] = {
+ # "arv": "http://arvados.org/cwl#"
+ #}
+
+ expect_container["mounts"]["/var/lib/cwl/workflow.json"]["content"]["$graph"][0]["steps"][0]["run"] = "keep:df44f9dd4b9467159f210f967e45417f+312/wf/submit_wf_process_properties.cwl"
- expect_container["properties"] = {
+ expect_container["properties"].update({
"baz": "blorp.txt",
"foo": "bar",
"quux": {
"q1": 1,
"q2": 2
}
- }
+ })
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_enable_preemptible(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--enable-preemptible",
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug', '--on-error=continue',
'--enable-preemptible',
- '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
stubs.expect_container_request_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_submit_disable_preemptible(self, stubs):
exited = arvados_cwl.main(
["--submit", "--no-wait", "--api=containers", "--debug", "--disable-preemptible",
expect_container = copy.deepcopy(stubs.expect_container_spec)
expect_container['command'] = ['arvados-cwl-runner', '--local', '--api=containers',
- '--no-log-timestamps', '--disable-validate', '--disable-color',
- '--eval-timeout=20', '--thread-count=0',
- '--enable-reuse', "--collection-cache-size=256", '--debug', '--on-error=continue',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug', '--on-error=continue',
'--disable-preemptible',
- '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
+ '/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(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+ @stubs()
+ def test_submit_container_prefer_cached_downloads(self, stubs):
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--prefer-cached-downloads",
+ "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',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug', "--on-error=continue", '--prefer-cached-downloads',
+ '/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(stubs.capture_stdout.getvalue(),
+ stubs.expect_container_request_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+ @stubs()
+ def test_submit_container_varying_url_params(self, stubs):
+ exited = arvados_cwl.main(
+ ["--submit", "--no-wait", "--api=containers", "--debug", "--varying-url-params", "KeyId,Signature",
+ "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',
+ '--no-log-timestamps', '--disable-validate', '--disable-color',
+ '--eval-timeout=20', '--thread-count=0',
+ '--enable-reuse', "--collection-cache-size=256",
+ '--output-name=Output from workflow submit_wf.cwl (%s)' % stubs.git_props["arv:gitDescribe"],
+ '--debug', "--on-error=continue", "--varying-url-params=KeyId,Signature",
+ '/var/lib/cwl/workflow.json#main', '/var/lib/cwl/cwl.input.json']
stubs.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher(expect_container))
class TestCreateWorkflow(unittest.TestCase):
existing_workflow_uuid = "zzzzz-7fd4e-validworkfloyml"
expect_workflow = StripYAMLComments(
- open("tests/wf/expect_upload_packed.cwl").read().rstrip())
+ open("tests/wf/expect_upload_wrapper.cwl").read().rstrip())
+ expect_workflow_altname = StripYAMLComments(
+ open("tests/wf/expect_upload_wrapper_altname.cwl").read().rstrip())
def setUp(self):
cwltool.process._names = set()
- arvados_cwl.arvdocker.arv_docker_clear_cache()
+ #arvados_cwl.arvdocker.arv_docker_clear_cache()
def tearDown(self):
root_logger = logging.getLogger('')
handlers = [h for h in root_logger.handlers if not isinstance(h, arvados_cwl.executor.RuntimeStatusLoggingHandler)]
root_logger.handlers = handlers
- @stubs
+ @stubs()
def test_create(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
["--create-workflow", "--debug",
"--api=containers",
"--project-uuid", project_uuid,
+ "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
"--api=containers",
"--project-uuid", project_uuid,
"--name", "testing 123",
+ "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
"owner_uuid": project_uuid,
"name": "testing 123",
"description": "",
- "definition": self.expect_workflow,
+ "definition": self.expect_workflow_altname,
}
}
stubs.api.workflows().create.assert_called_with(
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_update(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--debug",
+ "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_update_name(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.workflows().get().execute.return_value = {"owner_uuid": project_uuid}
exited = arvados_cwl.main(
["--update-workflow", self.existing_workflow_uuid,
"--debug", "--name", "testing 123",
+ "--disable-git",
"tests/wf/submit_wf.cwl", "tests/submit_test_job.json"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
"workflow": {
"name": "testing 123",
"description": "",
- "definition": self.expect_workflow,
+ "definition": self.expect_workflow_altname,
"owner_uuid": project_uuid
}
}
self.existing_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_collection_per_tool(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
["--create-workflow", "--debug",
"--api=containers",
"--project-uuid", project_uuid,
+ "--disable-git",
"tests/collection_per_tool/collection_per_tool.cwl"],
stubs.capture_stdout, sys.stderr, api_client=stubs.api)
- toolfile = "tests/collection_per_tool/collection_per_tool_packed.cwl"
+ toolfile = "tests/collection_per_tool/collection_per_tool_wrapper.cwl"
expect_workflow = StripYAMLComments(open(toolfile).read().rstrip())
body = {
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_with_imports(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
- @stubs
+ @stubs()
def test_create_with_no_input(self, stubs):
project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
stubs.api.groups().get().execute.return_value = {"group_class": "project"}
self.assertEqual(stubs.capture_stdout.getvalue(),
stubs.expect_workflow_uuid + '\n')
self.assertEqual(exited, 0)
+
+ @stubs()
+ def test_create_map(self, stubs):
+ # test uploading a document that uses objects instead of arrays
+ # for certain fields like inputs and requirements.
+
+ project_uuid = 'zzzzz-j7d0g-zzzzzzzzzzzzzzz'
+ stubs.api.groups().get().execute.return_value = {"group_class": "project"}
+
+ exited = arvados_cwl.main(
+ ["--create-workflow", "--debug",
+ "--api=containers",
+ "--project-uuid", project_uuid,
+ "--disable-git",
+ "tests/wf/submit_wf_map.cwl", "tests/submit_test_job.json"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+
+ stubs.api.pipeline_templates().create.refute_called()
+ stubs.api.container_requests().create.refute_called()
+
+ expect_workflow = StripYAMLComments(
+ open("tests/wf/expect_upload_wrapper_map.cwl").read().rstrip())
+
+ body = {
+ "workflow": {
+ "owner_uuid": project_uuid,
+ "name": "submit_wf_map.cwl",
+ "description": "",
+ "definition": expect_workflow,
+ }
+ }
+ stubs.api.workflows().create.assert_called_with(
+ body=JsonDiffMatcher(body))
+
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ stubs.expect_workflow_uuid + '\n')
+ self.assertEqual(exited, 0)
+
+
+class TestPrintKeepDeps(unittest.TestCase):
+ @stubs()
+ def test_print_keep_deps(self, stubs):
+ # test --print-keep-deps which is used by arv-copy
+
+ exited = arvados_cwl.main(
+ ["--print-keep-deps", "--debug",
+ "tests/wf/submit_wf_map.cwl"],
+ stubs.capture_stdout, sys.stderr, api_client=stubs.api)
+
+ self.assertEqual(stubs.capture_stdout.getvalue(),
+ '["5d373e7629203ce39e7c22af98a0f881+52", "999999999999999999999999999999d4+99"]' + '\n')
+ self.assertEqual(exited, 0)
projects / arvados.git / blobdiff