def test_none_product_patterns(mongodb_settings, agave, pipelinejobs_config,
pipeline_uuid, random_dir_name, admin_token):
"""Confirm that product_patterns can be set to None without failure
"""
archive_path = '/sample/tacc-cloud/' + random_string(32)
mpj = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
archive_path=archive_path,
experiment_id='experiment.tacc.10001',
product_patterns=None,
archive_patterns=[]).setup()
mpj.cancel(token=admin_token)
def test_no_archive_and_product_patterns(mongodb_settings, agave,
pipelinejobs_config, pipeline_uuid,
random_dir_name, admin_token):
"""Confirm that archive_patterns and product_patterns can be entirely un-
specified without failure
"""
archive_path = '/sample/tacc-cloud/' + random_dir_name
mpj = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
archive_path=archive_path,
experiment_id='experiment.tacc.10001').setup()
mpj.cancel(token=admin_token)
def client_w_sample_archive_path(mongodb_settings, pipelinejobs_config, agave,
pipeline_uuid, admin_token):
mpj = ManagedPipelineJob(
mongodb_settings,
pipelinejobs_config,
agave=agave,
archive_path='/sample/tacc-cloud',
experiment_id='experiment.tacc.10001',
archive_patterns=[{
'patterns': ['.json$'],
'level': '2'
}],
product_patterns=[{
'patterns': ['.json$'],
'derived_using': [
'1092d775-0f7c-5b4d-970f-e739711d5f36',
'modified_ecoli_MG1655_refFlat_txt-0-1-0'
],
'derived_from': [
'105fb204-530b-5915-9fd6-caf88ca9ad8a',
'1058868c-340e-5d8c-b66e-9739cbcf8d36', './672.png',
'agave://data-sd2e-community/sample/tacc-cloud/dawnofman.jpg'
]
}])
return mpj
def client_w_param_data(mongodb_settings, pipelinejobs_config, agave,
pipeline_uuid, experiment_id, job_data):
return ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
experiment_id=experiment_id,
data=job_data)
def instanced_client_w_param(mongodb_settings, pipelinejobs_config, agave,
pipeline_uuid, experiment_id):
return ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
experiment_id=experiment_id,
instanced=True)
def test_pipejob_init_archive_path_custom(mongodb_settings,
pipelinejobs_config, agave,
pipeline_uuid):
"""Checks that passing archive_path=<val> overrides generated value
"""
base = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
archive_path='/products/v2/test123')
assert base.archive_path.startswith('/products/v2')
assert base.archive_path.endswith('test123')
def client_w_sample_archive_path_missed_ref(mongodb_settings,
pipelinejobs_config, agave,
pipeline_uuid, admin_token):
mpj = ManagedPipelineJob(
mongodb_settings,
pipelinejobs_config,
agave=agave,
archive_path='/sample/tacc-cloud',
experiment_id='experiment.tacc.10001',
archive_patterns=[{
'patterns': ['.json$'],
'level': '2'
}],
product_patterns=[{
'patterns': ['.json$'],
'derived_using': [
'1092d775-0f7c-5b4d-970f-e739711d5f36',
'modified_ecoli_MG1655_refFlat_txt-0-1-0'
],
'derived_from': [
'105fb204-530b-5915-9fd6-caf88ca9ad8a',
'1058868c-340e-5d8c-b66e-9739cbcf8d36', './672.png',
'agave://data-sd2e-community/sample/tacc-cloud/dawnofman.jpg'
]
}])
def initjob():
mpj.setup()
mpj.run(token=admin_token)
mpj.finish(token=admin_token)
return mpj
job = None
try:
job = initjob()
except ManagedPipelineJobError:
mpj.reset(token=admin_token, no_clear_path=True, permissive=True)
job = initjob()
# print('MPJ.UUID', job.uuid)
return job
def test_uuid_bypass_invalid_metadata(mongodb_settings, agave,
pipelinejobs_config, pipeline_uuid,
random_dir_name, admin_token):
"""Confirm that passing a UUID directly to ManagedPipelineJob metadata
binding stage bypasses identifier resolution"""
archive_path = '/sample/tacc-cloud/' + random_string(32)
ident = typeduuid.catalog_uuid('ThisCanNeverEverEverWork', 'experiment')
mpj = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
archive_path=archive_path,
experiment_id=ident,
product_patterns=[],
archive_patterns=[]).setup()
def test_invalid_metadata_child_of(mongodb_settings, agave,
pipelinejobs_config, pipeline_uuid,
random_dir_name, admin_token):
"""Confirm that passing an unknown identifier not in the database will
cause ManagedPipelineJob initialization to raise an Exception
"""
archive_path = '/sample/tacc-cloud/' + random_string(32)
with pytest.raises(ValueError):
mpj = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
archive_path=archive_path,
experiment_id='ThisCanNeverEverEverWork',
product_patterns=[],
archive_patterns=[]).setup()
def test_pipejob_inputs_list(mongodb_settings, pipelinejobs_config, agave,
pipeline_uuid):
inputs = [
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmggea748b_r1bsun4yb67e7/wt-control-1_0.00015_2.fcs',
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmggea748b_r1bsun4yb67e7/wt-control-1_0.0003_4.fcs'
]
base = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
inputs=inputs,
experiment_id='experiment.ginkgo.10001')
# Only the two inputs and the first parameter have resolvable UUID in the test data set
# The experiment_id will resolve as well
assert len(base.acted_on) == 2
def test_pipejob_data_parameters_resolve(mongodb_settings, pipelinejobs_config,
agave, pipeline_uuid):
data = {
'parameters': {
'param1':
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmggea748b_r1bsun4yb67e7/wt-control-1_0.00015_2.fcs',
'param2':
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmgdayg2yq_r1bsu7tb7bsuk/6389_0.0003_4.fcs'
}
}
base = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
data=data)
# Only the two inputs and the first parameter have resolvable UUID in the test data set
assert len(base.acted_on) == 2
def test_pipejob_data_inputs_list_resolve(mongodb_settings,
pipelinejobs_config, agave,
pipeline_uuid):
data = {
'inputs': [
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmggea748b_r1bsun4yb67e7/wt-control-1_0.00015_2.fcs',
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmgdayg2yq_r1bsu7tb7bsuk/6389_0.0003_4.fcs',
'/uploads/transcriptic/201808/yeast_gates/r1bsmgdayg2yq_r1bsu7tb7bsuk/6389_0.0003_4.fcs'
]
}
base = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
data=data)
# Only the first two inputs resolvable since the list context expects fully-qualified URIs
assert len(base.acted_on) == 2
def test_pipejob_inputs_expt_id(mongodb_settings, pipelinejobs_config, agave,
pipeline_uuid, recid, raises_exception):
inputs = [
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmggea748b_r1bsun4yb67e7/wt-control-1_0.00015_2.fcs',
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmggea748b_r1bsun4yb67e7/wt-control-1_0.0003_4.fcs'
]
base = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
inputs=inputs,
experiment_id=recid)
# Only the two inputs and the first parameter have resolvable UUID in the test data set
assert len(base.child_of) > 0
# The hashid value for measurement.tacc.0x00000000, the default
# Should NOT be present if we resolve measurements
assert '5pQxBkRrRe2GEPOWWZBq4LNQ' not in base._archive_path_els
assert '/106' in base.archive_path
def test_pipejob_data_params_refs_resolve(mongodb_settings,
pipelinejobs_config, agave,
pipeline_uuid):
data = {
'parameters': {
'structure': 'https://www.rcsb.org/structure/6N0V',
'protein': 'https://www.uniprot.org/uniprot/G0S6G2'
}
}
base = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
data=data)
# ^^ These references should be present in the database if test_stores_reference has been run
assert len(base.acted_on) == 0
assert len(base.acted_using) == 2
def test_pipejob_inputs_no_link_or_data(mongodb_settings, pipelinejobs_config,
agave, pipeline_uuid):
inputs = [
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmggea748b_r1bsun4yb67e7/wt-control-1_0.00015_2.fcs',
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmggea748b_r1bsun4yb67e7/wt-control-1_0.0003_4.fcs'
]
base = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
inputs=inputs)
# Only the two inputs and the first parameter have resolvable UUID in the test data set
assert len(base.child_of) > 0
# The hashid value for measurement.tacc.0x00000000, the default
assert '5pQxBkRrRe2GEPOWWZBq4LNQ' in base._archive_path_els
# The hashid value for an empty "data" dictionary
assert 'PAVpwrObxp5YjYRvrJOd5yVp' in base._archive_path_els
# Pipeline ID is exposed in the path because there is a 1:1 mapping
assert '/106' in base.archive_path
def test_pipejob_agave_uri_from_data(mongodb_settings, pipelinejobs_config,
agave, pipeline_uuid):
data = {
'inputs': [
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmggea748b_r1bsun4yb67e7/wt-control-1_0.00015_2.fcs',
'agave://data-sd2e-community/products/v1/41e1dec1-2940-5b04-bd9e-54af78f30774/aaf646a5-7c05-5ab3-a144-5563fca6830d/a4609424-508a-555c-9720-5ee3df44e777/whole-shrew-20181207T220030Z/output/output.csv'
],
'parameters': {
'p1':
'agave://data-sd2e-community/uploads/transcriptic/201808/yeast_gates/r1bsmggea748b_r1bsun4yb67e7/wt-control-1_0.0003_4.fcs',
'p2': '/uploads/456.txt'
}
}
base = ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
data=data)
# Only the two inputs and the first parameter have resolvable UUID in the test data set
assert len(base.acted_on) == 3
def main():
rx = Reactor()
mes = AttrDict(rx.context.message_dict)
mongodb_conn = rx.settings.mongodb
# ! This code fixes an edge case in JSON serialization
if mes == {}:
try:
jsonmsg = json.loads(rx.context.raw_message)
mes = AttrDict(jsonmsg)
except Exception as exc:
rx.on_failure('Failed to load JSON from message', exc)
# Check incoming message against the default JSON schema
try:
rx.validate_message(mes, permissive=False)
except Exception as exc:
rx.on_failure('Failed to validate message to schema', exc)
# Verify appId is known to Agave apps API. Requires the invoking
# user has a tenant admin role unless the appId is public
agave_job = mes.get('job_definition')
agave_appid = agave_job.get('appId')
agave_app_details = None
job_params = mes.get('parameters')
instanced_archive_path = mes.get('instanced', True)
rx.logger.info(
'Received request to manage execution of {}'.format(agave_appid))
try:
agave_app_details = rx.client.apps.get(appId=agave_appid)
except HTTPError as http_err:
rx.on_failure(
'{} is not a known Agave application'.format(
agave_appid), http_err)
except Exception as generic_exception:
rx.on_failure(
'Failed to look up Agave application', generic_exception)
# Look up the Pipeline record for this Agave appId.
#
# Note that this requires a convention where the standalone Agave app is
# registered in the Pipelines system with pipeline.id == agave.app.id
pipeline_uuid = None
try:
manager_stores = Manager.init_stores(mongodb_conn)
pipeline_rec = manager_stores['pipeline'].find_one_by_id(id=agave_appid)
if pipeline_rec is None:
raise ValueError("No 'pipelines' record found in database")
else:
pipeline_uuid = pipeline_rec.get('uuid')
except Exception as generic_exception:
rx.on_failure('Failed to resolve appId {} to a Pipeline record'.format(
agave_appid), generic_exception)
def cancel_job(message='an error occurred', exception=None):
"""Helper function to cancel a failed job
"""
fmt_message = 'PipelineJob {} canceled because {}'.format(
job_uuid, message)
try:
job.cancel()
except Exception as job_cancel_exception:
rx.logger.warning(
'Failed to cancel PipelineJob {} because {}'.format(
job_uuid, job_cancel_exception))
rx.on_failure(fmt_message, exception)
def fail_job(message='an error occurred', exception=None):
"""Helper function to fail a job
"""
fmt_message = 'PipelineJob {} failed because {}'.format(
job_uuid, message)
try:
job.fail(data={'message': message})
except Exception as job_fail_exception:
rx.logger.warning(
'Unable to update PipelineJob state for {} because {}'.format(
job_uuid, job_fail_exception))
rx.on_failure(fmt_message, exception)
# Initialize the ManagedPipelineJob. It will be in the jobs collection
# with a status of CREATED.
job = None
job_uuid = None
rx.logger.info('Building initial job.data')
init_data = agave_job
mes_data = mes.get('data', {})
for k, v in job_params.items():
if v is not None and isinstance(v, str):
init_data[k] = v
# init_data = {**init_data, **mes_data}
try:
job = ManagedPipelineJob(rx.settings.mongodb,
rx.settings.pipelines.job_manager_id,
rx.settings.pipelines.updates_nonce,
pipeline_uuid=pipeline_uuid,
data=init_data,
session=rx.nickname,
agent=rx.uid,
task=rx.execid,
instanced=instanced_archive_path,
archive_path_patterns=mes.get(
'index_patterns', []),
** job_params
)
job.setup(mes_data)
job_uuid = job.uuid
except Exception as generic_exception:
if job is not None:
cancel_job(message='Failed to set up ManagedPipelineJob',
exception=generic_exception)
else:
rx.on_failure('Failed to set up ManagedPipelineJob', generic_exception)
# Extend the incoming Agave job definition to update the PipelineJob.
# Set the archivePath and archiveSystem from the ManagedPipelineJob
#
# The former is accomplished by adding custom notifications built from
# the job's 'callback' property, which was initialized on job.setup(). Any
# pre-existing notifications (email, other callbacks) are preserved.
try:
if 'notifications' not in agave_job:
agave_job['notifications'] = list()
# for event in ('SUBMITTING', 'STAGING_JOB', 'RUNNING', 'ARCHIVING', 'ARCHIVING_FINIS', 'FINISHED', 'FAILED'):
# Capture all Agave job states
notification = {'event': '*',
'persistent': True,
'url': job.callback + '&status=${STATUS}¬e=${JOB_ERROR}'}
agave_job['notifications'].append(notification)
notification = {'event': 'FINISHED',
'persistent': False,
'url': job.indexer_callback}
agave_job['notifications'].append(notification)
agave_job['archiveSystem'] = job.archive_system
agave_job['archivePath'] = job.archive_path
agave_job['archive'] = True
except Exception as generic_exception:
cancel_job(
message='Failed to prepare Agave job definition',
exception=generic_exception)
if rx.local:
print(json.dumps(agave_job, indent=4))
sys.exit(0)
# Launch the Agave job
agave_job_id = None
try:
resp = rx.client.jobs.submit(body=agave_job)
agave_job_id = None
if 'id' in resp:
agave_job_id = resp['id']
else:
raise KeyError('Invalid response received from jobs.submit()')
except HTTPError as h:
http_err_resp = agaveutils.process_agave_httperror(h)
fail_job(
message='Encountered API error: {}'.format(http_err_resp),
exception=HTTPError)
except Exception as job_submit_exception:
fail_job(message='Failed to launch {}'.format(
agave_appid), exception=job_submit_exception)
# Update the PipelineJob status
#
# This will create an entry in its history with an explicit link to
# the job asset. If this doesn't succeed, we don't fail the job since
# the expensive part (the Agave job) has been submitted.
try:
job_uri = job.canonicalize_job(agave_job_id)
job.run(data={'job_link': job_uri})
except Exception as job_update_exception:
rx.logger.warning(
'Unable to update status of job {} because {}'.format(
job_uuid, job_update_exception))
# If no other exit state has been encountered, report success
rx.on_success('ManagedPipelineJob {} is managing Agave job {} ({} usec)'.format(
job_uuid, agave_job_id, rx.elapsed()))
def client_w_archive_path(mongodb_settings, pipelinejobs_config, agave,
pipeline_uuid):
return ManagedPipelineJob(mongodb_settings,
pipelinejobs_config,
agave=agave,
archive_path='/products/v2/test123')