def pipeline():
"""POST a pipeline job (JSON) to run on the Luigi pipeline."""
if not request.data:
return 'POST a JSON pipeline config to execute or an id to GET. Body should be pipeline JSON'
try:
init()
p_cfg = PipelineConfig.from_dict(request.get_json())
p_id = insert_pipeline_config(p_cfg, util.conn_string)
if p_id == -1:
return '{ "success", false }'
job_id = jobs.create_new_job(jobs.NlpJob(job_id=-1, name=p_cfg.name, description=p_cfg.description,
owner=p_cfg.owner, status=jobs.STARTED, date_ended=None,
phenotype_id=-1, pipeline_id=p_id,
date_started=datetime.now(),
job_type='PIPELINE'), util.conn_string)
luigi_runner.run_pipeline(
p_cfg.config_type, str(p_id), job_id, p_cfg.owner)
output = dict()
output["pipeline_id"] = str(p_id)
output["job_id"] = str(job_id)
output["luigi_task_monitoring"] = "%s/static/visualiser/index.html#search__search=job=%s" % (
util.luigi_url, str(job_id))
output["status_endpoint"] = "%s/status/%s" % (
util.main_url, str(job_id))
output["results_endpoint"] = "%s/job_results/%s/%s" % (
util.main_url, str(job_id), 'pipeline')
return json.dumps(output, indent=4)
except Exception as ex:
return 'Failed to load and insert pipeline. ' + str(ex), 400
def pipeline():
"""POST a pipeline job (JSON) to run on the Luigi pipeline."""
if not request.data:
return 'POST a JSON pipeline config to execute or an id to GET. Body should be pipeline JSON'
try:
init()
p_cfg = PipelineConfig.from_dict(request.get_json())
p_id = insert_pipeline_config(p_cfg, util.conn_string)
if p_id == -1:
return '{ "success", false }'
job_id = jobs.create_new_job(jobs.NlpJob(job_id=-1, name=p_cfg.name, description=p_cfg.description,
owner=p_cfg.owner, status=jobs.STARTED, date_ended=None,
phenotype_id=-1, pipeline_id=p_id,
date_started=datetime.now(),
job_type='PIPELINE'), util.conn_string)
luigi_runner.run_pipeline(p_cfg.config_type, str(p_id), job_id, p_cfg.owner)
output = dict()
output["pipeline_id"] = str(p_id)
output["job_id"] = str(job_id)
output["luigi_task_monitoring"] = "%s/static/visualiser/index.html#search__search=job=%s" % (
util.luigi_url, str(job_id))
output["status_endpoint"] = "%s/status/%s" % (util.main_url, str(job_id))
output["results_endpoint"] = "%s/job_results/%s/%s" % (util.main_url, str(job_id), 'pipeline')
return json.dumps(output, indent=4)
except Exception as ex:
return 'Failed to load and insert pipeline. ' + str(ex), 400