def test_access_run_result_files_local(database, tmpdir):
"""Test accessing run result files."""
# -- Setup ----------------------------------------------------------------
env = Config().basedir(tmpdir).auth()
fs = FS(env=env)
workflow_id, group_id, run_id, user_id = success_run(database, fs, tmpdir)
local_service = LocalAPIFactory(env=env, db=database, engine=StateEngine())
# -- Read result files ----------------------------------------------------
with local_service(user_id=user_id) as api:
# Map file names to file handles.
r = api.runs().get_run(run_id=run_id)
files = dict()
for fh in r['files']:
files[fh['name']] = fh['id']
# Read content of result files.
fh = api.runs().get_result_file(run_id=run_id,
file_id=files['run/results/B.json'])
results = util.read_object(fh.open())
assert results == {'B': 1}
# -- Error when user 2 attempts to read file ------------------------------
with database.session() as session:
user_2 = create_user(session, active=True)
with local_service(user_id=user_2) as api:
with pytest.raises(err.UnauthorizedAccessError):
api.runs().get_result_file(run_id=run_id,
file_id=files['run/results/B.json'])
# -- With an open access policy user 2 can read the data file -------------
env = Config().basedir(tmpdir).open_access()
local_service = LocalAPIFactory(env=env, db=database, engine=StateEngine())
with local_service(user_id=user_2) as api:
api.runs().get_result_file(run_id=run_id,
file_id=files['run/results/B.json'])
def test_cancel_remote_workflow(tmpdir):
"""Cancel the execution of a remote workflow."""
# -- Setup ----------------------------------------------------------------
#
env = Config().basedir(tmpdir)
engine = RemoteTestController(client=RemoteTestClient(runcount=100),
poll_interval=1,
is_async=True)
service = LocalAPIFactory(env=env, engine=engine)
engine.service = service
# -- Start a new run for the workflow template.
with service() as api:
workflow_id = create_workflow(api, source=TEMPLATE_DIR)
user_id = create_user(api)
with service(user_id=user_id) as api:
group_id = create_group(api, workflow_id)
run_id = start_run(api, group_id)
# -- Poll workflow state every second.
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
while run['state'] == st.STATE_PENDING:
time.sleep(1)
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
serialize.validate_run_handle(run, state=st.STATE_RUNNING)
with service(user_id=user_id) as api:
api.runs().cancel_run(run_id=run_id, reason='test')
# Sleep to ensure that the workflow monitor polls the state and makes an
# attempt to update the run state. This should raise an error for the
# monitor. The error is not propagated here or to the run.
time.sleep(3)
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
serialize.validate_run_handle(run, state=st.STATE_CANCELED)
assert run['messages'][0] == 'test'
def test_run_remote_workflow_error(is_async, tmpdir):
"""Execute the remote workflow example synchronized and in asynchronous
mode when execution results in an error state.
"""
# -- Setup ----------------------------------------------------------------
env = Config().volume(FStore(basedir=str(tmpdir))).auth()
engine = RemoteWorkflowController(client=RemoteTestClient(
runcount=3, error='some error'),
poll_interval=0.1,
is_async=is_async)
service = LocalAPIFactory(env=env, engine=engine)
# Need to set the association between the engine and the service explicitly
# after the API is created.
engine.service = service
with service() as api:
workflow_id = create_workflow(api, source=BENCHMARK_DIR)
user_id = create_user(api)
with service(user_id=user_id) as api:
group_id = create_group(api, workflow_id)
# -- Unit test ------------------------------------------------------------
# Start a new run
with service(user_id=user_id) as api:
run_id = start_run(api, group_id)
# Poll workflow state every second.
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
watch_dog = 30
while run['state'] in st.ACTIVE_STATES and watch_dog:
time.sleep(1)
watch_dog -= 1
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
serialize.validate_run_handle(run, state=st.STATE_ERROR)
assert run['messages'] == ['some error']
def test_run_remote_workflow_with_error(tmpdir):
"""Execute the remote workflow example that will end in an error state in
asynchronous mode.
"""
# -- Setup ----------------------------------------------------------------
#
# Start a new run for the workflow template.
env = Config().basedir(tmpdir)
engine = RemoteTestController(client=RemoteTestClient(runcount=3,
error='some error'),
poll_interval=1,
is_async=True)
service = LocalAPIFactory(env=env, engine=engine)
engine.service = service
with service() as api:
workflow_id = create_workflow(api, source=TEMPLATE_DIR)
user_id = create_user(api)
with service(user_id=user_id) as api:
group_id = create_group(api, workflow_id)
run_id = start_run(api, group_id)
# Poll workflow state every second.
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
while run['state'] in st.ACTIVE_STATES:
time.sleep(1)
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
serialize.validate_run_handle(run, state=st.STATE_ERROR)
assert run['messages'][0] == 'some error'
def ClientAPI(
env: Optional[Dict] = None, basedir: Optional[str] = None,
database: Optional[str] = None, open_access: Optional[bool] = None,
run_async: Optional[bool] = None, user_id: Optional[str] = None
) -> APIFactory:
"""Create an instance of the API factory that is responsible for generating
API instances for a flowserv client.
The main distinction here is whether a connection is made to a local instance
of the service or to a remote instance. This distinction is made based on
the value of the FLOWSERV_CLIENT environment variable that takes the values
'local' or 'remote'. The default is 'local'.
Provides the option to alter the default settings of environment variables.
Parameters
----------
env: dict, default=None
Dictionary with configuration parameter values.
basedir: string, default=None
Base directory for all workflow files. If no directory is given or
specified in the environment a temporary directory will be created.
database: string, default=None
Optional database connect url.
open_access: bool, default=None
Use an open access policy if set to True.
run_async: bool, default=False
Run workflows in asynchronous mode.
user_id: string, default=None
Optional identifier for the authenticated API user.
Returns
-------
flowserv.service.api.APIFactory
"""
# Get the base configuration settings from the environment if not given.
env = env if env is not None else config.env()
if not isinstance(env, Config):
env = Config(env)
# Update configuration based on the given optional arguments.
if basedir is not None:
env.basedir(basedir)
if database is not None:
env.database(database)
if open_access is not None and open_access:
env.open_access()
# By default, the client runs all workflows synchronously.
if run_async is not None and run_async:
env.run_async()
elif env.get(config.FLOWSERV_ASYNC) is None:
env.run_sync()
# Create local or remote API factory depending on the FLOWSERV_CLIENT value.
client = env.get(config.FLOWSERV_CLIENT, config.LOCAL_CLIENT)
if client == config.LOCAL_CLIENT:
return LocalAPIFactory(env=env, user_id=user_id)
elif client == config.REMOTE_CLIENT:
# Not implemented yet.
pass
raise ValueError("inalid client type '{}'".format(client))
def test_postproc_workflow_errors(tmpdir):
"""Execute the modified helloworld example."""
# -- Setup ----------------------------------------------------------------
#
# It is important here that we do not use the SQLite in-memory database
# since this fails (for unknown reason; presumably due to different threads)
# when the post-processing run is updated.
# --
env = Config().basedir(tmpdir).run_async().auth()
service = LocalAPIFactory(env=env)
# Error during data preparation
run_erroneous_workflow(service, SPEC_FILE_ERR_1)
# Erroneous specification
run_erroneous_workflow(service, SPEC_FILE_ERR_2)
def test_result_archive_local(database, tmpdir):
"""Test getting an archive of run results."""
# -- Setup ----------------------------------------------------------------
env = Config().basedir(tmpdir).auth()
fs = FS(env=env)
workflow_id, group_id, run_id, user_id = success_run(database, fs, tmpdir)
local_service = LocalAPIFactory(env=env, db=database, engine=StateEngine())
# -- Get result archive ---------------------------------------------------
with local_service(user_id=user_id) as api:
archive = api.runs().get_result_archive(run_id=run_id)
tar = tarfile.open(fileobj=archive.open(), mode='r:gz')
members = [t.name for t in tar.getmembers()]
assert len(members) == 2
assert 'A.json' in members
assert 'run/results/B.json' in members
def test_cancel_remote_workflow(tmpdir):
"""Cancel the execution of a remote workflow."""
# -- Setup ----------------------------------------------------------------
env = Config().volume(FStore(basedir=str(tmpdir))).auth()
engine = RemoteWorkflowController(client=RemoteTestClient(runcount=100),
poll_interval=0.25,
is_async=True)
service = LocalAPIFactory(env=env, engine=engine)
# Need to set the association between the engine and the service explicitly
# after the API is created.
engine.service = service
with service() as api:
workflow_id = create_workflow(api, source=BENCHMARK_DIR)
user_id = create_user(api)
with service(user_id=user_id) as api:
group_id = create_group(api, workflow_id)
# -- Unit test ------------------------------------------------------------
# Start a new run
with service(user_id=user_id) as api:
run_id = start_run(api, group_id)
# -- Poll workflow state every second.
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
watch_dog = 30
while run['state'] == st.STATE_PENDING and watch_dog:
time.sleep(0.1)
watch_dog -= 1
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
serialize.validate_run_handle(run, state=st.STATE_RUNNING)
with service(user_id=user_id) as api:
api.runs().cancel_run(run_id=run_id, reason='test')
# Sleep to ensure that the workflow monitor polls the state and makes an
# attempt to update the run state. This should raise an error for the
# monitor. The error is not propagated here or to the run.
time.sleep(1)
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
serialize.validate_run_handle(run, state=st.STATE_CANCELED)
assert run['messages'][0] == 'test'
def test_run_remote_workflow(tmpdir, is_async):
"""Execute the remote workflow example synchronized and in asynchronous
mode.
"""
# -- Setup ----------------------------------------------------------------
#
env = Config().basedir(tmpdir)
engine = RemoteTestController(client=RemoteTestClient(runcount=3,
data=['success']),
poll_interval=1,
is_async=is_async)
service = LocalAPIFactory(env=env, engine=engine)
engine.service = service
# Start a new run for the workflow template.
with service() as api:
workflow_id = create_workflow(api, source=TEMPLATE_DIR)
user_id = create_user(api)
with service(user_id=user_id) as api:
group_id = create_group(api, workflow_id)
run_id = start_run(api, group_id)
# Poll workflow state every second.
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
watch_dog = 30
while run['state'] in st.ACTIVE_STATES and watch_dog:
time.sleep(1)
watch_dog -= 1
with service(user_id=user_id) as api:
run = api.runs().get_run(run_id=run_id)
serialize.validate_run_handle(run, state=st.STATE_SUCCESS)
files = dict()
for obj in run['files']:
files[obj['name']] = obj['id']
f_id = files['results/data.txt']
with service(user_id=user_id) as api:
fh = api.runs().get_result_file(run_id=run_id, file_id=f_id)
data = fh.open().read().decode('utf-8')
assert 'success' in data
def local_service(database, tmpdir):
"""Create a local API factory for test purposes."""
env = Config().basedir(tmpdir).volume(FStore(basedir=str(tmpdir))).auth()
return LocalAPIFactory(env=env, db=database, engine=StateEngine())
def sync_service(database, tmpdir):
"""Create a local API factory that executes workflows synchronously."""
env = Config().basedir(tmpdir).volume(
FStore(basedir=str(tmpdir))).run_sync().auth()
return LocalAPIFactory(env=env, db=database)
def test_postproc_workflow(fsconfig, tmpdir):
"""Execute the modified helloworld example."""
# -- Setup ----------------------------------------------------------------
#
# It is important here that we do not use the SQLite in-memory database
# since this fails (for unknown reason; presumably due to different threads)
# when the post-processing run is updated.
# --
env = Config().basedir(tmpdir).run_async().auth()
env.update(fsconfig)
service = LocalAPIFactory(env=env)
# Start a new run for the workflow template.
with service() as api:
# Need to set the file store in the backend to the new instance as
# well. Otherwise, the post processing workflow may attempt to use
# the backend which was initialized prior with a different file store.
workflow_id = create_workflow(
api,
source=TEMPLATE_DIR,
specfile=SPEC_FILE
)
user_id = create_user(api)
# Create four groups and run the workflow with a slightly different input
# file
for i in range(4):
with service(user_id=user_id) as api:
group_id = create_group(api, workflow_id)
names = io_file(data=NAMES[:(i + 1)], format='plain/text')
file_id = upload_file(api, group_id, names)
# Set the template argument values
arguments = [
serialize_arg('names', serialize_fh(file_id)),
serialize_arg('greeting', 'Hi')
]
run_id = start_run(api, group_id, arguments=arguments)
# Poll workflow state every second.
run = poll_run(service, run_id, user_id)
assert run['state'] == st.STATE_SUCCESS
with service() as api:
wh = api.workflows().get_workflow(workflow_id=workflow_id)
attmpts = 0
while 'postproc' not in wh:
time.sleep(1)
with service() as api:
wh = api.workflows().get_workflow(workflow_id=workflow_id)
attmpts += 1
if attmpts > 60:
break
assert 'postproc' in wh
serialize.validate_workflow_handle(wh)
attmpts = 0
while wh['postproc']['state'] in st.ACTIVE_STATES:
time.sleep(1)
with service() as api:
wh = api.workflows().get_workflow(workflow_id=workflow_id)
attmpts += 1
if attmpts > 60:
break
serialize.validate_workflow_handle(wh)
with service() as api:
ranking = api.workflows().get_ranking(workflow_id=workflow_id)
serialize.validate_ranking(ranking)
for fobj in wh['postproc']['files']:
if fobj['name'] == 'results/compare.json':
file_id = fobj['id']
with service(user_id=user_id) as api:
fh = api.workflows().get_result_file(
workflow_id=workflow_id,
file_id=file_id
)
compare = util.read_object(fh.open())
assert len(compare) == (i + 1)
# Access the post-processing result files.
with service() as api:
fh = api.workflows().get_result_archive(workflow_id=workflow_id)
assert fh.name.startswith('run')
assert fh.mime_type == 'application/gzip'
def async_service(database, tmpdir):
"""Create a local API factory that executes workflows asynchronously."""
env = Config().basedir(tmpdir).run_async().auth()
return LocalAPIFactory(env=env)