def workflow_run_post_req(workflow_id):
"""Submits the workflow for execution
Parameters
----------
workflow_id : str
The workflow id
Returns
-------
dict of {str: str}
A dictionary of the form: {'status': str, 'message': str} in which
status is the status of the request ('error' or 'success') and message
is a human readable string with the error message in case that status
is 'error'.
"""
try:
wf = ProcessingWorkflow(workflow_id)
except QiitaDBUnknownIDError:
return {
'status': 'error',
'message': 'Workflow %s does not exist' % workflow_id
}
wf.submit()
return {'status': 'success', 'message': ''}
def test_workflow_handler_post_req(self):
params = ('{"max_barcode_errors": 1.5, "barcode_type": "golay_12", '
'"max_bad_run_length": 3, "phred_offset": "auto", '
'"rev_comp": false, "phred_quality_threshold": 3, '
'"input_data": 1, "rev_comp_barcode": false, '
'"rev_comp_mapping_barcodes": false, '
'"min_per_read_length_fraction": 0.75, "sequence_max_n": 0}')
obs = workflow_handler_post_req("*****@*****.**", 1, params)
wf_id = obs['workflow_id']
wf = ProcessingWorkflow(wf_id)
nodes = wf.graph.nodes()
self.assertEqual(len(nodes), 1)
job = nodes[0]
exp = {
'status': 'success',
'message': '',
'workflow_id': wf_id,
'job': {
'id': job.id,
'inputs': [1],
'label': "Split libraries FASTQ",
'outputs': [['demultiplexed', 'Demultiplexed']]
}
}
self.assertEqual(obs, exp)
def test_workflow_handler_post_req(self):
next_id = get_count('qiita.processing_job_workflow_root') + 1
obs = workflow_handler_post_req("*****@*****.**", 1, '{"input_data": 1}')
wf = ProcessingWorkflow(next_id)
nodes = wf.graph.nodes()
self.assertEqual(len(nodes), 1)
job = nodes[0]
exp = {
'status': 'success',
'message': '',
'workflow_id': next_id,
'job': {
'id': job.id,
'inputs': [1],
'label': "Split libraries FASTQ",
'outputs': [['demultiplexed', 'Demultiplexed']]
}
}
self.assertEqual(obs, exp)
def workflow_handler_patch_req(req_op,
req_path,
req_value=None,
req_from=None):
"""Patches a workflow
Parameters
----------
req_op : str
The operation to perform on the workflow
req_path : str
Path parameter with the workflow to patch
req_value : str, optional
The value that needs to be modified
req_from : str, optional
The original path of the element
Returns
-------
dict of {str: str}
A dictionary of the form: {'status': str, 'message': str} in which
status is the status of the request ('error' or 'success') and message
is a human readable string with the error message in case that status
is 'error'.
"""
if req_op == 'add':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 1:
return {'status': 'error', 'message': 'Incorrect path parameter'}
req_path = req_path[0]
try:
wf = ProcessingWorkflow(req_path)
except QiitaDBUnknownIDError:
return {
'status': 'error',
'message': 'Workflow %s does not exist' % req_path
}
req_value = loads(req_value)
dflt_params = DefaultParameters(req_value['dflt_params'])
req_params = req_value.get('req_params', None)
opt_params = req_value.get('opt_params', None)
connections = {
ProcessingJob(k): v
for k, v in req_value['connections'].items()
}
job = wf.add(dflt_params,
connections=connections,
req_params=req_params,
opt_params=opt_params)
job_cmd = job.command
return {
'status': 'success',
'message': '',
'job': {
'id': job.id,
'inputs': list(req_value['connections'].keys()),
'label': job_cmd.name,
'outputs': job_cmd.outputs
}
}
elif req_op == 'remove':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 2:
return {'status': 'error', 'message': 'Incorrect path parameter'}
wf_id = req_path[0]
job_id = req_path[1]
wf = ProcessingWorkflow(wf_id)
job = ProcessingJob(job_id)
wf.remove(job, cascade=True)
return {'status': 'success', 'message': ''}
else:
return {
'status':
'error',
'message':
'Operation "%s" not supported. Current supported '
'operations: add' % req_op
}
