def kill_workflow(experiment_id):
"""
.. http:post:: /api/experiments/(string:experiment_id)/workflow/kill
Kill all jobs of the currently running workflow.
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: application/json
{
"message": "ok"
}
:reqheader Authorization: JWT token issued by the server
:statuscode 200: no error
"""
logger.info('kill workflow for experiment %d', experiment_id)
workflow = gc3pie.retrieve_most_recent_task(experiment_id, 'workflow')
gc3pie.kill_task(workflow)
return jsonify(message='ok')
def get_job_output(experiment_id):
'''Gets output generated by a previous submission.'''
data = json.loads(request.data)
project = yaml.load(data['project'])
pipeline_description = PipelineDescription(**project['pipe']['description'])
handles_descriptions = {
h['name']: HandleDescriptions(**h['description'])
for h in project['handles']
}
jt = ImageAnalysisPipelineEngine(
experiment_id,
pipeline_description=pipeline_description,
handles_descriptions=handles_descriptions,
)
try:
jobs = gc3pie.retrieve_most_recent_task(experiment_id, 'jtui')
output = _get_output(experiment_id, jobs)
return jsonify(output=output)
except IndexError:
return jsonify(output=None)
def get_job_output(experiment_id):
'''Gets output generated by a previous submission.'''
data = json.loads(request.data)
project = yaml.load(data['project'])
pipeline_description = PipelineDescription(
**project['pipe']['description'])
handles_descriptions = {
h['name']: HandleDescriptions(**h['description'])
for h in project['handles']
}
jt = ImageAnalysisPipelineEngine(
experiment_id,
pipeline_description=pipeline_description,
handles_descriptions=handles_descriptions,
)
try:
jobs = gc3pie.retrieve_most_recent_task(experiment_id, 'jtui')
output = _get_output(experiment_id, jobs)
return jsonify(output=output)
except IndexError:
return jsonify(output=None)
def resubmit_workflow(experiment_id):
"""
.. http:post:: /api/experiments/(string:experiment_id)/workflow/resubmit
Resubmit a workflow for an experiment providing a new
:class:`WorkflowDescription <tmlib.workflow.description.WorkflowDescription>`
in YAML format and optionally an ``index`` of a stage at which the
workflow should be resubmitted.
**Example request**:
.. sourcecode:: http
Content-Type: application/json
{
"description": {...},
"index": 1
}
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: application/json
{
"message": "ok",
"submission_id": 1
}
:reqheader Authorization: JWT token issued by the server
:statuscode 400: malformed request
:statuscode 200: no error
"""
logger.info('resubmit workflow for experiment %d', experiment_id)
data = json.loads(request.data)
logger.debug(
"/experiments/%s/workflow/resubmit:"
" Received data:\n"
"========\n"
"%s"
"\n========", experiment_id, request.data)
index = data.get('index')
stage_name = data.get('stage_name')
with tm.utils.ExperimentSession(experiment_id) as session:
experiment = _retrieve_experiment_or_abort(experiment_id, session)
if 'description' in data:
logger.info('use provided workflow description')
workflow_description = WorkflowDescription(**data['description'])
experiment.persist_workflow_description(workflow_description)
else:
logger.info('load workflow description')
workflow_description = experiment.workflow_description
logger.debug(
"/experiments/%s/workflow/resubmit:"
" Using workflow description:\n"
"========\n"
"%r"
"\n========", experiment_id, workflow_description)
if stage_name is None and index is None:
index = 0
elif index is not None:
index = int(index)
elif stage_name is not None:
indices = [
i for i, d in enumerate(workflow_description.stages)
if d.name == stage_name and d.active
]
if len(indices) == 0:
raise MalformedRequestError(
'The specified stage "%s" does not exist or is not set active.'
% stage_name)
index = indices[0]
else:
raise MalformedRequestError(
'Only one of the following parameters can be specified in the '
'request body: "index", "stage_name"')
workflow = gc3pie.retrieve_most_recent_task(experiment_id, 'workflow')
workflow.update_description(workflow_description)
workflow.update_stage(index)
gc3pie.resubmit_task(workflow, index)
return jsonify({'message': 'ok', 'submission_id': workflow.submission_id})
def resubmit_workflow(experiment_id):
"""
.. http:post:: /api/experiments/(string:experiment_id)/workflow/resubmit
Resubmit a workflow for an experiment providing a new
:class:`WorkflowDescription <tmlib.workflow.description.WorkflowDescription>`
in YAML format and optionally an ``index`` of a stage at which the
workflow should be resubmitted.
**Example request**:
.. sourcecode:: http
Content-Type: application/json
{
"description": {...},
"index": 1
}
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: application/json
{
"message": "ok",
"submission_id": 1
}
:reqheader Authorization: JWT token issued by the server
:statuscode 400: malformed request
:statuscode 200: no error
"""
logger.info('resubmit workflow for experiment %d', experiment_id)
data = json.loads(request.data)
index = data.get('index')
stage_name = data.get('stage_name')
with tm.utils.ExperimentSession(experiment_id) as session:
experiment = _retrieve_experiment_or_abort(experiment_id, session)
if 'description' in data:
logger.info('use provided workflow description')
workflow_description = WorkflowDescription(**data['description'])
experiment.persist_workflow_description(workflow_description)
else:
logger.info('load workflow description')
workflow_description = experiment.workflow_description
if stage_name is None and index is None:
index = 0
elif index is not None:
index = int(index)
elif stage_name is not None:
indices = [
i for i, d in enumerate(workflow_description.stages)
if d.name == stage_name and d.active
]
if len(indices) == 0:
raise MalformedRequestError(
'The specified stage "%s" does not exist or is not set active.'
% stage_name
)
index = indices[0]
else:
raise MalformedRequestError(
'Only one of the following parameters can be specified in the '
'request body: "index", "stage_name"'
)
workflow = gc3pie.retrieve_most_recent_task(experiment_id, 'workflow')
# sanity check -- the job daemon will report the same error, but
# at that point it'd be too late to report to HTTP API clients
total_stages = len(workflow.tasks)
if index <= total_stages:
if (index > 0 and not workflow.tasks[index-1].is_terminated):
raise MalformedRequestError(
'Cannot resubmit workflow from stage %d:'
' the preceding stage (task ID %s)'
' has not completed running yet.'
% (index, workflow.tasks[index-1].persistent_id)
)
else:
raise MalformedRequestError(
'Workflow has only %d stages, cannot resubmit from stage %d'
% (total_stages, index)
)
workflow.update_description(workflow_description)
workflow.update_stage(index)
gc3pie.resubmit_task(workflow, index)
return jsonify({
'message': 'ok',
'submission_id': workflow.submission_id
})
def resubmit_workflow(experiment_id):
"""
.. http:post:: /api/experiments/(string:experiment_id)/workflow/resubmit
Resubmit a workflow for an experiment providing a new
:class:`WorkflowDescription <tmlib.workflow.description.WorkflowDescription>`
in YAML format and optionally an ``index`` of a stage at which the
workflow should be resubmitted.
**Example request**:
.. sourcecode:: http
Content-Type: application/json
{
"description": {...},
"index": 1
}
**Example response**:
.. sourcecode:: http
HTTP/1.1 200 OK
Content-Type: application/json
{
"message": "ok",
"submission_id": 1
}
:reqheader Authorization: JWT token issued by the server
:statuscode 400: malformed request
:statuscode 200: no error
"""
logger.info('resubmit workflow for experiment %d', experiment_id)
data = json.loads(request.data)
index = data.get('index')
stage_name = data.get('stage_name')
with tm.utils.ExperimentSession(experiment_id) as session:
experiment = _retrieve_experiment_or_abort(experiment_id, session)
if 'description' in data:
logger.info('use provided workflow description')
workflow_description = WorkflowDescription(**data['description'])
experiment.persist_workflow_description(workflow_description)
else:
logger.info('load workflow description')
workflow_description = experiment.workflow_description
if stage_name is None and index is None:
index = 0
elif index is not None:
index = int(index)
elif stage_name is not None:
indices = [
i for i, d in enumerate(workflow_description.stages)
if d.name == stage_name and d.active
]
if len(indices) == 0:
raise MalformedRequestError(
'The specified stage "%s" does not exist or is not set active.'
% stage_name)
index = indices[0]
else:
raise MalformedRequestError(
'Only one of the following parameters can be specified in the '
'request body: "index", "stage_name"')
workflow = gc3pie.retrieve_most_recent_task(experiment_id, 'workflow')
# sanity check -- the job daemon will report the same error, but
# at that point it'd be too late to report to HTTP API clients
total_stages = len(workflow.tasks)
if index <= total_stages:
if (index > 0 and not workflow.tasks[index - 1].is_terminated):
raise MalformedRequestError(
'Cannot resubmit workflow from stage %d:'
' the preceding stage (task ID %s)'
' has not completed running yet.' %
(index, workflow.tasks[index - 1].persistent_id))
else:
raise MalformedRequestError(
'Workflow has only %d stages, cannot resubmit from stage %d' %
(total_stages, index))
workflow.update_description(workflow_description)
workflow.update_stage(index)
gc3pie.resubmit_task(workflow, index)
return jsonify({'message': 'ok', 'submission_id': workflow.submission_id})