def get_script_pipeline_fragment(dbm):
'''Get a fragment of a pipeline
Script -> AnnoTask:
A Script connected to an AnnoTask
Returns:
:class:`lost.db.model.PipeElement`, :class:`lost.db.model.PipeElement`, :class:`lost.db.model.Pipe`:
(script_element, annotation_task_element, pipeline)
'''
pipe = model.Pipe(name='TestPipe')
dbm.add(pipe)
dbm.commit()
script = model.Script(name='TestScript', path='data/pipes/test/test.py')
dbm.add(script)
dbm.commit()
pe_s = model.PipeElement(pipe_id=pipe.idx, dtype=dtype.PipeElement.SCRIPT)
pe_s.script = script
dbm.add(pe_s)
dbm.commit()
script_result = model.Result()
dbm.add(script_result)
dbm.commit()
anno_task = model.AnnoTask(name='TestAnnoTask')
dbm.add(anno_task)
pe_a = model.PipeElement(pipe_id=pipe.idx,
dtype=dtype.PipeElement.ANNO_TASK)
pe_a.anno_task = anno_task
# pe_a.result_in.append(script_result)
# pe_a.result_out.append(script_result)
dbm.add(pe_a)
dbm.commit()
# pe_s.pe_outs.append(pe_a)
# dbm.commit()
# Link elements
res_link_s = model.ResultLink(result_id=script_result.idx,
pe_n=pe_s.idx,
pe_out=pe_a.idx)
res_link_a = model.ResultLink(result_id=script_result.idx,
pe_n=pe_a.idx,
pe_out=None)
dbm.add(res_link_s)
dbm.add(res_link_a)
dbm.commit()
return pe_s, pe_a, pipe
def __init__(self, template, data, manager_id, group_id):
self.pipe = model.Pipe()
self.data_map = dict()
self.pe_map = dict()
self.template_map = dict()
self.template = template
self.data = data
self.manager_id = manager_id
self.group_id = group_id
self.timestamp_now = datetime.now()
self.template_content = json.loads(template.json_template)
for element in self.template_content['elements']:
self.template_map[element['peN']] = element
for element in self.data['elements']:
self.data_map[element['peN']] = element
def create_pipe(self):
try:
is_debug_mode = self.data['isDebug']
except KeyError:
is_debug_mode = False
pipe = model.Pipe(name=self.data['name'],
pipe_template_id=self.template.idx,
state=state.Pipe.PENDING,
is_locked=True,
description=self.data['description'],
manager_id=self.manager_id,
is_debug_mode=is_debug_mode,
group_id=self.group_id,
timestamp=self.timestamp_now,
start_definition=json.dumps(self.data))
self.pipe = pipe
return pipe