def test_workflow_handler_patch_req_error(self):
# Incorrect path parameter
obs = workflow_handler_patch_req('add', '/1/extra/')
exp = {'status': 'error',
'message': 'Incorrect path parameter'}
self.assertEqual(obs, exp)
# Workflow does not exist
obs = workflow_handler_patch_req('add', '/1000/')
exp = {'status': 'error',
'message': 'Workflow 1000 does not exist'}
self.assertEqual(obs, exp)
# Operation not supported
obs = workflow_handler_patch_req('replace', '/1/')
exp = {'status': 'error',
'message': 'Operation "replace" not supported. '
'Current supported operations: add'}
self.assertEqual(obs, exp)
# Incorrect path parameter (op = remove)
obs = workflow_handler_patch_req('remove', '/1/')
exp = {'status': 'error',
'message': 'Incorrect path parameter'}
self.assertEqual(obs, exp)
def test_workflow_handler_patch_req_error(self):
# Incorrect path parameter
obs = workflow_handler_patch_req('add', '/1/extra/')
exp = {'status': 'error', 'message': 'Incorrect path parameter'}
self.assertEqual(obs, exp)
# Workflow does not exist
obs = workflow_handler_patch_req('add', '/1000/')
exp = {'status': 'error', 'message': 'Workflow 1000 does not exist'}
self.assertEqual(obs, exp)
# Operation not supported
obs = workflow_handler_patch_req('replace', '/1/')
exp = {
'status':
'error',
'message':
'Operation "replace" not supported. '
'Current supported operations: add'
}
self.assertEqual(obs, exp)
# Incorrect path parameter (op = remove)
obs = workflow_handler_patch_req('remove', '/1/')
exp = {'status': 'error', 'message': 'Incorrect path parameter'}
self.assertEqual(obs, exp)
def test_workflow_handler_patch_req(self):
# Create a new workflow so it is in construction
exp_command = Command(1)
json_str = (
'{"input_data": 1, "max_barcode_errors": 1.5, '
'"barcode_type": "golay_12", "max_bad_run_length": 3, '
'"rev_comp": false, "phred_quality_threshold": 3, '
'"rev_comp_barcode": false, "rev_comp_mapping_barcodes": false, '
'"min_per_read_length_fraction": 0.75, "sequence_max_n": 0}')
exp_params = Parameters.load(exp_command, json_str=json_str)
exp_user = User('*****@*****.**')
name = "Test processing workflow"
# tests success
wf = ProcessingWorkflow.from_scratch(exp_user,
exp_params,
name=name,
force=True)
graph = wf.graph
nodes = list(graph.nodes())
job_id = nodes[0].id
value = {
'dflt_params': 10,
'connections': {
job_id: {
'demultiplexed': 'input_data'
}
}
}
obs = workflow_handler_patch_req('add',
'/%s/' % wf.id,
req_value=dumps(value))
new_jobs = set(wf.graph.nodes()) - set(nodes)
self.assertEqual(len(new_jobs), 1)
new_job = new_jobs.pop()
exp = {
'status': 'success',
'message': '',
'job': {
'id': new_job.id,
'inputs': [job_id],
'label': 'Pick closed-reference OTUs',
'outputs': [['OTU table', 'BIOM']]
}
}
self.assertEqual(obs, exp)
obs = workflow_handler_patch_req('remove',
'/%s/%s/' % (wf.id, new_job.id))
exp = {'status': 'success', 'message': ''}
jobs = set(wf.graph.nodes()) - set(nodes)
self.assertEqual(jobs, set())
def test_workflow_handler_patch_req(self):
# Create a new workflow so it is in construction
exp_command = Command(1)
json_str = (
'{"input_data": 1, "max_barcode_errors": 1.5, '
'"barcode_type": "golay_12", "max_bad_run_length": 3, '
'"rev_comp": false, "phred_quality_threshold": 3, '
'"rev_comp_barcode": false, "rev_comp_mapping_barcodes": false, '
'"min_per_read_length_fraction": 0.75, "sequence_max_n": 0}')
exp_params = Parameters.load(exp_command, json_str=json_str)
exp_user = User('*****@*****.**')
name = "Test processing workflow"
# tests success
wf = ProcessingWorkflow.from_scratch(
exp_user, exp_params, name=name, force=True)
graph = wf.graph
nodes = list(graph.nodes())
job_id = nodes[0].id
value = {'dflt_params': 10,
'connections': {job_id: {'demultiplexed': 'input_data'}}}
obs = workflow_handler_patch_req(
'add', '/%s/' % wf.id, req_value=dumps(value))
new_jobs = set(wf.graph.nodes()) - set(nodes)
self.assertEqual(len(new_jobs), 1)
new_job = new_jobs.pop()
exp = {'status': 'success',
'message': '',
'job': {'id': new_job.id,
'inputs': [job_id],
'label': 'Pick closed-reference OTUs',
'outputs': [['OTU table', 'BIOM']]}}
self.assertEqual(obs, exp)
obs = workflow_handler_patch_req(
'remove', '/%s/%s/' % (wf.id, new_job.id))
exp = {'status': 'success', 'message': ''}
jobs = set(wf.graph.nodes()) - set(nodes)
self.assertEqual(jobs, set())
