def check_job_finished(self, job_id=0, user=None):
from app.jobs.jobs import get_job
j = get_job(job_id)
history = self.get_history(j.get_output_parameter("history_id"))
if j.has_permission(user):
status = j.check_status()
if status == "complete":
history = self.get_history(
j.get_output_parameter("history_id"))
vs = ViewSet(self.db, self.get_viewset_id())
c_d = {"data": [], "columns": []}
if len(history["fields"]) > 0:
c_d = vs.get_columns_and_data(history["fields"])
graphs = []
tracks = []
for g in self.data["graph_config"]:
if g["id"] in history["graphs"]:
graphs.append(g)
for t in self.data["browser_config"]["state"]:
if t["track_id"] in history["tracks"]:
tracks.append(t)
return {
"status": "complete",
"columns": c_d["columns"],
"data": c_d["data"],
"tracks": tracks,
"graphs": graphs,
"history": history
}
else:
return {"status": status, "history": history}
def process_job(job_id, args=None):
from app.jobs.jobs import get_job
job = get_job(job_id)
if not args:
job.process()
else:
job.process(args)
def check_all_jobs():
types = job_types.keys()
jobs = db.session.query(UserJob).filter(
UserJob.status.notin_(['complete', 'failed', 'processing']),
UserJob.type.in_(types)).all()
for j in jobs:
try:
job = get_job(j.id)
job.check_status()
except Exception as e:
app.logger.exception("Unable to process job #{}".format(j.id))
def get_bw_stats_data(self, job_id=0):
from app.jobs.jobs import get_job
j = get_job(job_id)
wig_names = j.get_input_parameter("wig_names")
vs = ViewSet(self.db, self.get_viewset_id())
data = vs.get_wig_stats_data(wig_names)
wig_files = []
for track in self.data["browser_config"]["state"]:
if track['track_id'] in wig_names:
wig_files.append(track)
data["tracks"] = wig_files
return data
def reprocess_job(job_id):
j = get_job(job_id)
if j.has_permission(current_user):
j.process()
return ujson.dumps({
"status": j.job.status,
"info": {
"inputs": j.job.inputs,
"outputs": j.job.outputs
},
"success": True
})
else:
return ujson.dumps({
"success": False,
"msg": "You do not have permission"
})
def get_cluster_data(self, job_id=0):
from app.jobs.jobs import get_job
j = get_job(job_id)
name = j.get_input_parameter("name")
methods = j.get_input_parameter("methods")
vs = ViewSet(self.db, self.get_viewset_id())
data = vs.get_cluster_data(name, methods)
graph_ids = []
graphs = []
field_graph = name + "_fields"
for method in methods:
graph_ids.append(name + "_" + method)
for graph in self.data["graph_config"]:
if graph['id'] in graph_ids:
graphs.append(graph)
if graph["id"] == field_graph:
graphs.append(graph)
data["graphs"] = graphs
return data
def get_job_info(job_id):
j = get_job(job_id)
return ujson.dumps(j.get_info())
def get_job_status(id):
job = get_job(int(id))
if not job.has_permission(current_user):
return ujson.dumps({"success": False, "msg": "Permission denied"})
return ujson.dumps({"success": True, "status": job.job.status})