def test_default_work_api(self):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = copy.deepcopy(get_rootDesc())
runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'containers')
def test_default_work_api(self):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = copy.deepcopy(get_rootDesc())
del api._rootDesc.get('resources')['jobs']['methods']['create']
runner = arvados_cwl.ArvCwlRunner(api)
self.assertEqual(runner.work_api, 'containers')
def test_default_work_api(self):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = copy.deepcopy(get_rootDesc())
del api._rootDesc.get('resources')['jobs']['methods']['create']
runner = arvados_cwl.ArvCwlRunner(api)
self.assertEqual(runner.work_api, 'containers')
def test_run(self, list_images_in_arv, mockcollection,
mockcollectionreader):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
runner = arvados_cwl.ArvCwlRunner(api)
self.assertEqual(runner.work_api, 'jobs')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {
"portable_data_hash": "99999999999999999999999999999993+99"
}
runner.api.collections().list().execute.return_vaulue = {
"items": [{
"portable_data_hash":
"99999999999999999999999999999993+99"
}]
}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
make_fs_access = functools.partial(
arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
document_loader.fetcher_constructor = functools.partial(
arvados_cwl.CollectionFetcher,
api_client=api,
fs_access=make_fs_access(""))
document_loader.fetcher = document_loader.fetcher_constructor(
document_loader.cache, document_loader.session)
document_loader.fetch_text = document_loader.fetcher.fetch_text
document_loader.check_exists = document_loader.fetcher.check_exists
tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
mockcollection(
).portable_data_hash.return_value = "99999999999999999999999999999999+118"
arvtool = arvados_cwl.ArvadosWorkflow(runner,
tool,
work_api="jobs",
avsc_names=avsc_names,
basedir="",
make_fs_access=make_fs_access,
loader=document_loader,
makeTool=runner.arv_make_tool,
metadata=metadata)
arvtool.formatgraph = None
it = arvtool.job({},
mock.MagicMock(),
basedir="",
make_fs_access=make_fs_access)
it.next().run()
it.next().run()
with open("tests/wf/scatter2_subwf.cwl") as f:
subwf = StripYAMLComments(f.read())
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher(
{
'minimum_script_version':
'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script_version': 'master',
'script': 'crunchrunner',
'script_parameters': {
'tasks': [{
'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'
},
'task.vwd': {
'workflow.cwl':
'$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
'cwl.input.yml':
'$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
},
'command': [
u'cwltool', u'--no-container',
u'--move-outputs',
u'--preserve-entire-environment',
u'workflow.cwl#main', u'cwl.input.yml'
],
'task.stdout':
'cwl.output.json'
}]
},
'runtime_constraints': {
'min_scratch_mb_per_node': 2048,
'min_cores_per_node': 1,
'docker_image': 'arvados/jobs',
'min_ram_mb_per_node': 1024
},
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'
}),
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
[
'script_version', 'in git',
'a3f2cb186e437bfce0031b024b2157b73ed2717d'
], ['docker_image_locator', 'in docker', 'arvados/jobs']],
find_or_create=True)
mockcollection().open().__enter__().write.assert_has_calls(
[mock.call(subwf)])
mockcollection().open().__enter__().write.assert_has_calls([
mock.call('''{
"fileblub": {
"basename": "token.txt",
"class": "File",
"location": "/keep/99999999999999999999999999999999+118/token.txt"
},
"sleeptime": 5
}''')
])
def test_resource_requirements(self, list_images_in_arv):
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
arvados_cwl.add_arv_hints()
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {
"portable_data_hash": "99999999999999999999999999999993+99"
}
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
tool = {
"inputs": [],
"outputs": [],
"hints": [{
"class": "ResourceRequirement",
"coresMin": 3,
"ramMin": 3000,
"tmpdirMin": 4000
}, {
"class": "http://arvados.org/cwl#RuntimeConstraints",
"keep_cache": 512,
"outputDirType": "keep_output_dir"
}, {
"class": "http://arvados.org/cwl#APIRequirement",
}, {
"class": "http://arvados.org/cwl#ReuseRequirement",
"enableReuse": False
}],
"baseCommand":
"ls"
}
make_fs_access = functools.partial(
arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner,
tool,
work_api="jobs",
avsc_names=avsc_names,
make_fs_access=make_fs_access,
loader=Loader({}))
arvtool.formatgraph = None
for j in arvtool.job({},
mock.MagicMock(),
basedir="",
make_fs_access=make_fs_access):
j.run(enable_reuse=True)
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher({
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'runtime_constraints': {},
'script_parameters': {
'tasks': [{
'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'
},
'task.keepTmpOutput': True,
'command': ['ls']
}]
},
'script_version': 'master',
'minimum_script_version':
'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
'docker_image': 'arvados/jobs',
'min_cores_per_node': 3,
'min_ram_mb_per_node': 3512, # ramMin + keep_cache
'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
'keep_cache_mb_per_task': 512
}
}),
find_or_create=False,
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
[
'script_version', 'in git',
'a3f2cb186e437bfce0031b024b2157b73ed2717d'
], ['docker_image_locator', 'in docker', 'arvados/jobs']])
def test_resource_requirements(self):
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
arvados_cwl.add_arv_hints()
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
tool = {
"inputs": [],
"outputs": [],
"hints": [{
"class": "ResourceRequirement",
"coresMin": 3,
"ramMin": 3000,
"tmpdirMin": 4000
}, {
"class": "http://arvados.org/cwl#RuntimeConstraints",
"keep_cache": 512,
"outputDirType": "keep_output_dir"
}, {
"class": "http://arvados.org/cwl#APIRequirement",
}],
"baseCommand":
"ls"
}
make_fs_access = functools.partial(arvados_cwl.CollectionFsAccess,
api_client=runner.api)
arvtool = arvados_cwl.ArvadosCommandTool(runner,
tool,
work_api="jobs",
avsc_names=avsc_names,
make_fs_access=make_fs_access,
loader=Loader({}))
arvtool.formatgraph = None
for j in arvtool.job({},
mock.MagicMock(),
basedir="",
make_fs_access=make_fs_access):
j.run()
runner.api.jobs().create.assert_called_with(
body={
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'runtime_constraints': {},
'script_parameters': {
'tasks': [{
'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'
},
'task.keepTmpOutput': True,
'command': ['ls']
}]
},
'script_version': 'master',
'minimum_script_version':
'9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
'docker_image': 'arvados/jobs',
'min_cores_per_node': 3,
'min_ram_mb_per_node': 3000,
'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
'keep_cache_mb_per_task': 512
}
},
find_or_create=True,
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
[
'script_version', 'in git',
'9e5b98e8f5f4727856b53447191f9c06e3da2ba6'
], ['docker_image_locator', 'in docker', 'arvados/jobs']])
def test_run(self, mockcollection):
try:
arvados_cwl.add_arv_hints()
runner = arvados_cwl.ArvCwlRunner(mock.MagicMock())
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(
"v1.0")
tool, metadata = document_loader.resolve_ref(
"tests/wf/scatter2.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
mockcollection(
).portable_data_hash.return_value = "99999999999999999999999999999999+118"
make_fs_access = functools.partial(arvados_cwl.CollectionFsAccess,
api_client=runner.api)
arvtool = arvados_cwl.ArvadosWorkflow(
runner,
tool,
work_api="jobs",
avsc_names=avsc_names,
basedir="",
make_fs_access=make_fs_access,
loader=document_loader,
makeTool=runner.arv_make_tool,
metadata=metadata)
arvtool.formatgraph = None
it = arvtool.job({},
mock.MagicMock(),
basedir="",
make_fs_access=make_fs_access)
it.next().run()
it.next().run()
with open("tests/wf/scatter2_subwf.cwl") as f:
subwf = f.read()
mockcollection().open().__enter__().write.assert_has_calls(
[mock.call(subwf)])
mockcollection().open().__enter__().write.assert_has_calls(
[mock.call('{sleeptime: 5}')])
runner.api.jobs(
).create.assert_called_with(body={
'minimum_script_version':
'9e5b98e8f5f4727856b53447191f9c06e3da2ba6',
'repository':
'arvados',
'script_version':
'master',
'script':
'crunchrunner',
'script_parameters': {
'tasks': [{
'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'
},
'task.vwd': {
'workflow.cwl':
'$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
'cwl.input.yml':
'$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
},
'command': [
u'cwltool', u'--no-container', u'--move-outputs',
u'--preserve-entire-environment',
u'workflow.cwl#main', u'cwl.input.yml'
],
'task.stdout':
'cwl.output.json'
}]
},
'runtime_constraints': {
'min_scratch_mb_per_node': 2048,
'min_cores_per_node': 1,
'docker_image': 'arvados/jobs',
'min_ram_mb_per_node': 1024
},
'owner_uuid':
'zzzzz-8i9sb-zzzzzzzzzzzzzzz'
},
filters=
[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
[
'script_version', 'in git',
'9e5b98e8f5f4727856b53447191f9c06e3da2ba6'
],
[
'docker_image_locator',
'in docker', 'arvados/jobs'
]],
find_or_create=True)
except:
logging.exception("")
def test_resource_requirements(self, list_images_in_arv):
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
arvados_cwl.add_arv_hints()
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
tool = {
"inputs": [],
"outputs": [],
"hints": [{
"class": "ResourceRequirement",
"coresMin": 3,
"ramMin": 3000,
"tmpdirMin": 4000
}, {
"class": "http://arvados.org/cwl#RuntimeConstraints",
"keep_cache": 512,
"outputDirType": "keep_output_dir"
}, {
"class": "http://arvados.org/cwl#APIRequirement",
}],
"baseCommand": "ls"
}
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
make_fs_access=make_fs_access, loader=Loader({}))
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
j.run()
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher({
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'runtime_constraints': {},
'script_parameters': {
'tasks': [{
'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
'task.keepTmpOutput': True,
'command': ['ls']
}]
},
'script_version': 'master',
'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
'docker_image': 'arvados/jobs',
'min_cores_per_node': 3,
'min_ram_mb_per_node': 3512, # ramMin + keep_cache
'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
'keep_cache_mb_per_task': 512
}
}),
find_or_create=True,
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
['docker_image_locator', 'in docker', 'arvados/jobs']])
def test_resource_requirements(self, list_images_in_arv):
runner = mock.MagicMock()
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
arvados_cwl.add_arv_hints()
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
tool = {
"inputs": [],
"outputs": [],
"hints": [{
"class": "ResourceRequirement",
"coresMin": 3,
"ramMin": 3000,
"tmpdirMin": 4000
}, {
"class": "http://arvados.org/cwl#RuntimeConstraints",
"keep_cache": 512,
"outputDirType": "keep_output_dir"
}, {
"class": "http://arvados.org/cwl#APIRequirement",
},
{
"class": "http://arvados.org/cwl#ReuseRequirement",
"enableReuse": False
}],
"baseCommand": "ls",
"id": "#",
"class": "CommandLineTool"
}
loadingContext, runtimeContext = self.helper(runner)
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, loadingContext)
arvtool.formatgraph = None
for j in arvtool.job({}, mock.MagicMock(), runtimeContext):
j.run(runtimeContext)
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher({
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz',
'runtime_constraints': {},
'script_parameters': {
'tasks': [{
'task.env': {'HOME': '$(task.outdir)', 'TMPDIR': '$(task.tmpdir)'},
'task.keepTmpOutput': True,
'command': ['ls']
}]
},
'script_version': 'master',
'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script': 'crunchrunner',
'runtime_constraints': {
'docker_image': 'arvados/jobs',
'min_cores_per_node': 3,
'min_ram_mb_per_node': 3512, # ramMin + keep_cache
'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
'keep_cache_mb_per_task': 512
}
}),
find_or_create=False,
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
['docker_image_locator', 'in docker', 'arvados/jobs']])
def run():
# Timestamps are added by crunch-job, so don't print redundant timestamps.
arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
# Print package versions
logger.info(arvados_cwl.versionstring())
api = arvados.api("v1")
arvados_cwl.add_arv_hints()
runner = None
try:
job_order_object = arvados.current_job()['script_parameters']
toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
def keeppath(v):
if pdh_path.match(v):
return "keep:%s" % v
else:
return v
def keeppathObj(v):
if "location" in v:
v["location"] = keeppath(v["location"])
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = {
"class": "File",
"location": "keep:%s" % v
}
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
output_name = None
output_tags = None
enable_reuse = True
on_error = "continue"
debug = False
if "arv:output_name" in job_order_object:
output_name = job_order_object["arv:output_name"]
del job_order_object["arv:output_name"]
if "arv:output_tags" in job_order_object:
output_tags = job_order_object["arv:output_tags"]
del job_order_object["arv:output_tags"]
if "arv:enable_reuse" in job_order_object:
enable_reuse = job_order_object["arv:enable_reuse"]
del job_order_object["arv:enable_reuse"]
if "arv:on_error" in job_order_object:
on_error = job_order_object["arv:on_error"]
del job_order_object["arv:on_error"]
if "arv:debug" in job_order_object:
debug = job_order_object["arv:debug"]
del job_order_object["arv:debug"]
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.safeapi.ThreadSafeApiCache(
api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
output_name=output_name, output_tags=output_tags)
make_fs_access = functools.partial(CollectionFsAccess,
collection_cache=runner.collection_cache)
t = load_tool(toolpath, runner.arv_make_tool,
fetcher_constructor=functools.partial(CollectionFetcher,
api_client=runner.api,
fs_access=make_fs_access(""),
num_retries=runner.num_retries))
if debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
logging.getLogger("cwltool").setLevel(logging.DEBUG)
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.on_error = on_error
args.submit = False
args.debug = debug
args.quiet = False
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
args.make_fs_access = make_fs_access
args.trash_intermediate = False
args.intermediate_output_ttl = 0
args.priority = arvados_cwl.DEFAULT_PRIORITY
args.do_validate = True
args.disable_js_validation = False
runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)
else:
logging.exception("Unhandled exception")
if runner and runner.final_output_collection:
outputCollection = runner.final_output_collection.portable_data_hash()
else:
outputCollection = None
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
'output': outputCollection,
'success': False,
'progress':1.0
}).execute()
def test_overall_resource_singlecontainer(self, list_images_in_arv,
mockcollection,
mockcollectionreader):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'jobs')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {
"portable_data_hash": "99999999999999999999999999999993+99"
}
runner.api.collections().list().execute.return_vaulue = {
"items": [{
"portable_data_hash":
"99999999999999999999999999999993+99"
}]
}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
loadingContext, runtimeContext = self.helper(runner)
tool, metadata = loadingContext.loader.resolve_ref(
"tests/wf/echo-wf.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(
mock.MagicMock(), *args, **kwargs)
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
it = arvtool.job({}, mock.MagicMock(), runtimeContext)
it.next().run(runtimeContext)
it.next().run(runtimeContext)
with open("tests/wf/echo-subwf.cwl") as f:
subwf = StripYAMLComments(f.read())
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher(
{
'minimum_script_version':
'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script_version': 'master',
'script': 'crunchrunner',
'script_parameters': {
'tasks': [{
'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'
},
'task.vwd': {
'workflow.cwl':
'$(task.keep)/99999999999999999999999999999996+99/workflow.cwl',
'cwl.input.yml':
'$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml'
},
'command': [
u'cwltool', u'--no-container',
u'--move-outputs',
u'--preserve-entire-environment',
u'workflow.cwl#main', u'cwl.input.yml'
],
'task.stdout':
'cwl.output.json'
}]
},
'runtime_constraints': {
'min_scratch_mb_per_node': 4096,
'min_cores_per_node': 3,
'docker_image': 'arvados/jobs',
'min_ram_mb_per_node': 1024
},
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'
}),
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
[
'script_version', 'in git',
'a3f2cb186e437bfce0031b024b2157b73ed2717d'
], ['docker_image_locator', 'in docker', 'arvados/jobs']],
find_or_create=True)
def run():
# Timestamps are added by crunch-job, so don't print redundant timestamps.
arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
# Print package versions
logger.info(arvados_cwl.versionstring())
api = arvados.api("v1")
arvados_cwl.add_arv_hints()
runner = None
try:
job_order_object = arvados.current_job()['script_parameters']
toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
def keeppath(v):
if pdh_path.match(v):
return "keep:%s" % v
else:
return v
def keeppathObj(v):
if "location" in v:
v["location"] = keeppath(v["location"])
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = {
"class": "File",
"location": "keep:%s" % v
}
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
output_name = None
output_tags = None
enable_reuse = True
on_error = "continue"
debug = False
if "arv:output_name" in job_order_object:
output_name = job_order_object["arv:output_name"]
del job_order_object["arv:output_name"]
if "arv:output_tags" in job_order_object:
output_tags = job_order_object["arv:output_tags"]
del job_order_object["arv:output_tags"]
if "arv:enable_reuse" in job_order_object:
enable_reuse = job_order_object["arv:enable_reuse"]
del job_order_object["arv:enable_reuse"]
if "arv:on_error" in job_order_object:
on_error = job_order_object["arv:on_error"]
del job_order_object["arv:on_error"]
if "arv:debug" in job_order_object:
debug = job_order_object["arv:debug"]
del job_order_object["arv:debug"]
arvargs = argparse.Namespace()
arvargs.work_api = "jobs"
arvargs.output_name = output_name
arvargs.output_tags = output_tags
arvargs.thread_count = 1
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.safeapi.ThreadSafeApiCache(
api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
arvargs=arvargs)
make_fs_access = functools.partial(CollectionFsAccess,
collection_cache=runner.collection_cache)
t = load_tool(toolpath, runner.loadingContext)
if debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
logging.getLogger("cwltool").setLevel(logging.DEBUG)
args = ArvRuntimeContext(vars(arvargs))
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.on_error = on_error
args.submit = False
args.debug = debug
args.quiet = False
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
args.make_fs_access = make_fs_access
args.trash_intermediate = False
args.intermediate_output_ttl = 0
args.priority = arvados_cwl.DEFAULT_PRIORITY
args.do_validate = True
args.disable_js_validation = False
args.tmp_outdir_prefix = "tmp"
runner.arv_executor(t, job_order_object, args, logger=logger)
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)
else:
logging.exception("Unhandled exception")
if runner and runner.final_output_collection:
outputCollection = runner.final_output_collection.portable_data_hash()
else:
outputCollection = None
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
'output': outputCollection,
'success': False,
'progress':1.0
}).execute()
def run():
# Timestamps are added by crunch-job, so don't print redundant timestamps.
arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
# Print package versions
logger.info(arvados_cwl.versionstring())
api = arvados.api("v1")
arvados_cwl.add_arv_hints()
runner = None
try:
job_order_object = arvados.current_job()['script_parameters']
toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
def keeppath(v):
if pdh_path.match(v):
return "keep:%s" % v
else:
return v
def keeppathObj(v):
if "location" in v:
v["location"] = keeppath(v["location"])
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = {
"class": "File",
"location": "keep:%s" % v
}
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
output_name = None
output_tags = None
enable_reuse = True
on_error = "continue"
if "arv:output_name" in job_order_object:
output_name = job_order_object["arv:output_name"]
del job_order_object["arv:output_name"]
if "arv:output_tags" in job_order_object:
output_tags = job_order_object["arv:output_tags"]
del job_order_object["arv:output_tags"]
if "arv:enable_reuse" in job_order_object:
enable_reuse = job_order_object["arv:enable_reuse"]
del job_order_object["arv:enable_reuse"]
if "arv:on_error" in job_order_object:
on_error = job_order_object["arv:on_error"]
del job_order_object["arv:on_error"]
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
output_name=output_name, output_tags=output_tags)
make_fs_access = functools.partial(CollectionFsAccess,
collection_cache=runner.collection_cache)
t = load_tool(toolpath, runner.arv_make_tool,
fetcher_constructor=functools.partial(CollectionFetcher,
api_client=runner.api,
fs_access=make_fs_access(""),
num_retries=runner.num_retries))
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.on_error = on_error
args.submit = False
args.debug = False
args.quiet = False
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
args.make_fs_access = make_fs_access
runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)
else:
logging.exception("Unhandled exception")
if runner and runner.final_output_collection:
outputCollection = runner.final_output_collection.portable_data_hash()
else:
outputCollection = None
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
'output': outputCollection,
'success': False,
'progress':1.0
}).execute()
def run():
# Print package versions
logger.info(arvados_cwl.versionstring())
api = arvados.api("v1")
arvados_cwl.add_arv_hints()
runner = None
try:
job_order_object = arvados.current_job()['script_parameters']
pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
def keeppath(v):
if pdh_path.match(v):
return "keep:%s" % v
else:
return v
def keeppathObj(v):
v["location"] = keeppath(v["location"])
job_order_object["cwl:tool"] = "file://%s/%s" % (
os.environ['TASK_KEEPMOUNT'], job_order_object["cwl:tool"])
for k, v in job_order_object.items():
if isinstance(
v,
basestring) and arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = {
"class": "File",
"location": "keep:%s" % v
}
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
adjustDirObjs(
job_order_object,
functools.partial(
getListing,
arvados_cwl.fsaccess.CollectionFsAccess("", api_client=api)))
output_name = None
output_tags = None
enable_reuse = True
if "arv:output_name" in job_order_object:
output_name = job_order_object["arv:output_name"]
del job_order_object["arv:output_name"]
if "arv:output_tags" in job_order_object:
output_tags = job_order_object["arv:output_tags"]
del job_order_object["arv:output_tags"]
if "arv:enable_reuse" in job_order_object:
enable_reuse = job_order_object["arv:enable_reuse"]
del job_order_object["arv:enable_reuse"]
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api(
'v1', model=OrderedJsonModel()),
output_name=output_name,
output_tags=output_tags)
t = load_tool(job_order_object, runner.arv_make_tool)
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.submit = False
args.debug = True
args.quiet = False
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
args.cwl_runner_job = {
"uuid": arvados.current_job()["uuid"],
"state": arvados.current_job()["state"]
}
outputObj = runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)
else:
logging.exception("Unhandled exception")
if runner and runner.final_output_collection:
outputCollection = runner.final_output_collection.portable_data_hash(
)
else:
outputCollection = None
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
'output': outputCollection,
'success': False,
'progress': 1.0
}).execute()
def test_overall_resource_singlecontainer(self, list_images_in_arv, mockcollection, mockcollectionreader):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
runner = arvados_cwl.ArvCwlRunner(api)
self.assertEqual(runner.work_api, 'jobs')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
loadingContext, runtimeContext = self.helper(runner)
tool, metadata = loadingContext.loader.resolve_ref("tests/wf/echo-wf.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
it = arvtool.job({}, mock.MagicMock(), runtimeContext)
it.next().run(runtimeContext)
it.next().run(runtimeContext)
with open("tests/wf/echo-subwf.cwl") as f:
subwf = StripYAMLComments(f.read())
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher({
'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script_version': 'master',
'script': 'crunchrunner',
'script_parameters': {
'tasks': [{'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'},
'task.vwd': {
'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
},
'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
'task.stdout': 'cwl.output.json'}]},
'runtime_constraints': {
'min_scratch_mb_per_node': 4096,
'min_cores_per_node': 3,
'docker_image': 'arvados/jobs',
'min_ram_mb_per_node': 1024
},
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
['docker_image_locator', 'in docker', 'arvados/jobs']],
find_or_create=True)
def test_overall_resource_singlecontainer(self, list_images_in_arv,
mockcollection,
mockcollectionreader):
arv_docker_clear_cache()
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'containers')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_value = {
"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzz",
"portable_data_hash": "99999999999999999999999999999993+99"
}
runner.api.collections().list().execute.return_value = {
"items": [{
"uuid":
"zzzzz-4zz18-zzzzzzzzzzzzzzz",
"portable_data_hash":
"99999999999999999999999999999993+99"
}]
}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
runner.secret_store = cwltool.secrets.SecretStore()
loadingContext, runtimeContext = self.helper(runner)
runner.fs_access = runtimeContext.make_fs_access(
runtimeContext.basedir)
loadingContext.do_update = True
tool, metadata = loadingContext.loader.resolve_ref(
"tests/wf/echo-wf.cwl")
mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(
mock.MagicMock(), *args, **kwargs)
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
it = arvtool.job({}, mock.MagicMock(), runtimeContext)
next(it).run(runtimeContext)
next(it).run(runtimeContext)
with open("tests/wf/echo-subwf.cwl") as f:
subwf = StripYAMLComments(f.read())
runner.api.container_requests().create.assert_called_with(
body=JsonDiffMatcher({
'output_ttl':
0,
'environment': {
'HOME': '/var/spool/cwl',
'TMPDIR': '/tmp'
},
'scheduling_parameters': {},
'name':
u'echo-subwf',
'secret_mounts': {},
'runtime_constraints': {
'API': True,
'vcpus': 3,
'ram': 1073741824
},
'properties': {},
'priority':
500,
'mounts': {
'/var/spool/cwl/cwl.input.yml': {
'portable_data_hash':
'99999999999999999999999999999996+99',
'kind': 'collection',
'path': 'cwl.input.yml'
},
'/var/spool/cwl/workflow.cwl': {
'portable_data_hash':
'99999999999999999999999999999996+99',
'kind': 'collection',
'path': 'workflow.cwl'
},
'stdout': {
'path': '/var/spool/cwl/cwl.output.json',
'kind': 'file'
},
'/tmp': {
'kind': 'tmp',
'capacity': 1073741824
},
'/var/spool/cwl': {
'kind': 'tmp',
'capacity': 3221225472
}
},
'state':
'Committed',
'output_path':
'/var/spool/cwl',
'container_image':
'99999999999999999999999999999993+99',
'command': [
u'cwltool', u'--no-container', u'--move-outputs',
u'--preserve-entire-environment', u'workflow.cwl#main',
u'cwl.input.yml'
],
'use_existing':
True,
'output_name':
u'Output for step echo-subwf',
'cwd':
'/var/spool/cwl'
}))
def test_run(self, list_images_in_arv, mockcollection):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
runner = arvados_cwl.ArvCwlRunner(api)
self.assertEqual(runner.work_api, 'jobs')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
tool, metadata = document_loader.resolve_ref("tests/wf/scatter2.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
basedir="", make_fs_access=make_fs_access, loader=document_loader,
makeTool=runner.arv_make_tool, metadata=metadata)
arvtool.formatgraph = None
it = arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access)
it.next().run()
it.next().run()
with open("tests/wf/scatter2_subwf.cwl") as f:
subwf = f.read()
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher({
'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script_version': 'master',
'script': 'crunchrunner',
'script_parameters': {
'tasks': [{'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'},
'task.vwd': {
'workflow.cwl': '$(task.keep)/99999999999999999999999999999999+118/workflow.cwl',
'cwl.input.yml': '$(task.keep)/99999999999999999999999999999999+118/cwl.input.yml'
},
'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
'task.stdout': 'cwl.output.json'}]},
'runtime_constraints': {
'min_scratch_mb_per_node': 2048,
'min_cores_per_node': 1,
'docker_image': 'arvados/jobs',
'min_ram_mb_per_node': 1024
},
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
['docker_image_locator', 'in docker', 'arvados/jobs']],
find_or_create=True)
mockcollection().open().__enter__().write.assert_has_calls([mock.call(subwf)])
mockcollection().open().__enter__().write.assert_has_calls([mock.call(
'''{
"sleeptime": 5
}''')])
def test_run(self, list_images_in_arv, mockcollection,
mockcollectionreader):
arv_docker_clear_cache()
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'containers')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_value = {
"portable_data_hash": "99999999999999999999999999999993+99"
}
runner.api.collections().list().execute.return_value = {
"items": [{
"uuid":
"zzzzz-4zz18-zzzzzzzzzzzzzzz",
"portable_data_hash":
"99999999999999999999999999999993+99"
}]
}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
runner.secret_store = cwltool.secrets.SecretStore()
loadingContext, runtimeContext = self.helper(runner)
runner.fs_access = runtimeContext.make_fs_access(
runtimeContext.basedir)
tool, metadata = loadingContext.loader.resolve_ref(
"tests/wf/scatter2.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
mockc = mock.MagicMock()
mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(
mockc, *args, **kwargs)
mockcollectionreader().find.return_value = arvados.arvfile.ArvadosFile(
mock.MagicMock(), "token.txt")
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
it = arvtool.job({}, mock.MagicMock(), runtimeContext)
next(it).run(runtimeContext)
next(it).run(runtimeContext)
with open("tests/wf/scatter2_subwf.cwl") as f:
subwf = StripYAMLComments(f.read()).rstrip()
runner.api.container_requests(
).create.assert_called_with(body=JsonDiffMatcher({
"command": [
"cwltool", "--no-container", "--move-outputs",
"--preserve-entire-environment", "workflow.cwl#main",
"cwl.input.yml"
],
"container_image":
"99999999999999999999999999999993+99",
"cwd":
"/var/spool/cwl",
"environment": {
"HOME": "/var/spool/cwl",
"TMPDIR": "/tmp"
},
"mounts": {
"/keep/99999999999999999999999999999999+118": {
"kind": "collection",
"portable_data_hash":
"99999999999999999999999999999999+118"
},
"/tmp": {
"capacity": 1073741824,
"kind": "tmp"
},
"/var/spool/cwl": {
"capacity": 1073741824,
"kind": "tmp"
},
"/var/spool/cwl/cwl.input.yml": {
"kind": "collection",
"path": "cwl.input.yml",
"portable_data_hash": "99999999999999999999999999999996+99"
},
"/var/spool/cwl/workflow.cwl": {
"kind": "collection",
"path": "workflow.cwl",
"portable_data_hash": "99999999999999999999999999999996+99"
},
"stdout": {
"kind": "file",
"path": "/var/spool/cwl/cwl.output.json"
}
},
"name":
"scatterstep",
"output_name":
"Output for step scatterstep",
"output_path":
"/var/spool/cwl",
"output_ttl":
0,
"priority":
500,
"properties": {},
"runtime_constraints": {
"ram": 1073741824,
"vcpus": 1
},
"scheduling_parameters": {},
"secret_mounts": {},
"state":
"Committed",
"use_existing":
True
}))
mockc.open().__enter__().write.assert_has_calls([mock.call(subwf)])
mockc.open().__enter__().write.assert_has_calls([
mock.call('''{
"fileblub": {
"basename": "token.txt",
"class": "File",
"location": "/keep/99999999999999999999999999999999+118/token.txt",
"size": 0
},
"sleeptime": 5
}''')
])
def test_run(self, list_images_in_arv, mockcollection, mockcollectionreader):
arvados_cwl.add_arv_hints()
api = mock.MagicMock()
api._rootDesc = get_rootDesc()
runner = arvados_cwl.executor.ArvCwlExecutor(api)
self.assertEqual(runner.work_api, 'jobs')
list_images_in_arv.return_value = [["zzzzz-4zz18-zzzzzzzzzzzzzzz"]]
runner.api.collections().get().execute.return_vaulue = {"portable_data_hash": "99999999999999999999999999999993+99"}
runner.api.collections().list().execute.return_vaulue = {"items": [{"portable_data_hash": "99999999999999999999999999999993+99"}]}
runner.project_uuid = "zzzzz-8i9sb-zzzzzzzzzzzzzzz"
runner.ignore_docker_for_reuse = False
runner.num_retries = 0
loadingContext, runtimeContext = self.helper(runner)
tool, metadata = loadingContext.loader.resolve_ref("tests/wf/scatter2.cwl")
metadata["cwlVersion"] = tool["cwlVersion"]
mockc = mock.MagicMock()
mockcollection.side_effect = lambda *args, **kwargs: CollectionMock(mockc, *args, **kwargs)
mockcollectionreader().find.return_value = arvados.arvfile.ArvadosFile(mock.MagicMock(), "token.txt")
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, loadingContext)
arvtool.formatgraph = None
it = arvtool.job({}, mock.MagicMock(), runtimeContext)
next(it).run(runtimeContext)
next(it).run(runtimeContext)
with open("tests/wf/scatter2_subwf.cwl") as f:
subwf = StripYAMLComments(f.read())
runner.api.jobs().create.assert_called_with(
body=JsonDiffMatcher({
'minimum_script_version': 'a3f2cb186e437bfce0031b024b2157b73ed2717d',
'repository': 'arvados',
'script_version': 'master',
'script': 'crunchrunner',
'script_parameters': {
'tasks': [{'task.env': {
'HOME': '$(task.outdir)',
'TMPDIR': '$(task.tmpdir)'},
'task.vwd': {
'workflow.cwl': '$(task.keep)/99999999999999999999999999999996+99/workflow.cwl',
'cwl.input.yml': '$(task.keep)/99999999999999999999999999999996+99/cwl.input.yml'
},
'command': [u'cwltool', u'--no-container', u'--move-outputs', u'--preserve-entire-environment', u'workflow.cwl#main', u'cwl.input.yml'],
'task.stdout': 'cwl.output.json'}]},
'runtime_constraints': {
'min_scratch_mb_per_node': 2048,
'min_cores_per_node': 1,
'docker_image': 'arvados/jobs',
'min_ram_mb_per_node': 1024
},
'owner_uuid': 'zzzzz-8i9sb-zzzzzzzzzzzzzzz'}),
filters=[['repository', '=', 'arvados'],
['script', '=', 'crunchrunner'],
['script_version', 'in git', 'a3f2cb186e437bfce0031b024b2157b73ed2717d'],
['docker_image_locator', 'in docker', 'arvados/jobs']],
find_or_create=True)
mockc.open().__enter__().write.assert_has_calls([mock.call(subwf)])
mockc.open().__enter__().write.assert_has_calls([mock.call(
bytes(b'''{
"fileblub": {
"basename": "token.txt",
"class": "File",
"location": "/keep/99999999999999999999999999999999+118/token.txt",
"size": 0
},
"sleeptime": 5
}'''))])
