def main(args):
log = lutils.setupLog('worksetlogger', args.logfile)
session = get_session()
if args.ws:
step = session.query(Process).filter_by(luid=args.ws).one()
ws = lclasses.Workset_SQL(session, log, step)
with open(args.conf) as conf_file:
conf = yaml.load(conf_file, Loader=yaml.SafeLoader)
couch = lutils.setupServer(conf)
db = couch["worksets"]
doc = {}
for row in db.view('worksets/lims_id')[ws.obj['id']]:
doc = db.get(row.id)
final_doc = lutils.merge(ws.obj, doc)
db.save(final_doc)
elif args.recent:
recent_processes = get_last_modified_processes(
session, [8, 46, 117, 204, 1454, 1908], args.interval)
processes_to_update = set()
for p in recent_processes:
if p.typeid in [
117, 204
] and p.daterun: #will only catch finished setup workset plate
processes_to_update.add(p)
else:
processes_to_update.update(
get_processes_in_history(session, p.processid, [117, 204]))
log.info("the following processes will be updated : {0}".format(
processes_to_update))
lpar.masterProcessSQL(args, processes_to_update, log)
def main(ws_id):
log = lutils.setupLog('worksetlogger', "out.log")
lims = Lims(BASEURI, USERNAME, PASSWORD)
wsp = gent.Process(lims, id=ws_id)
lc = lclasses.LimsCrawler(lims, wsp)
lc.crawl()
ws1 = lclasses.Workset(lims, lc, log)
session = get_session()
step = session.query(Process).filter_by(luid=ws_id).one()
ws2 = lclasses.Workset_SQL(session, log, step)
diffs = my_comp(ws1.obj, ws2.obj)
if diffs:
print "\n".join(diffs)
#print "##########################"
#pprint(ws1.obj)
#print "##########################"
#pprint(ws2.obj)
else:
print "no diff found"
def processWSULSQL(args, queue, logqueue):
work=True
session=get_session()
with open(args.conf) as conf_file:
conf=yaml.load(conf_file, Loader=yaml.SafeLoader)
couch=lutils.setupServer(conf)
db=couch["worksets"]
procName = mp.current_process().name
proclog = logging.getLogger(procName)
proclog.setLevel(level=logging.INFO)
mfh = QueueHandler(logqueue)
mft = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
mfh.setFormatter(mft)
proclog.addHandler(mfh)
while work:
#grabs project from queue
try:
ws_id = queue.get(block=True, timeout=3)
proclog.info("Starting work on {}".format(ws_id))
except Queue.Empty:
work = False
proclog.info("exiting gracefully")
break
else:
step=session.query(gt.Process).filter(gt.Process.processid == int(ws_id)).one()
ws=lclasses.Workset_SQL(session, proclog, step)
doc={}
for row in db.view('worksets/lims_id')[ws.obj['id']]:
doc=db.get(row.id)
if doc:
final_doc=lutils.merge(ws.obj, doc)
else:
final_doc=ws.obj
#clean possible name duplicates
for row in db.view('worksets/name')[ws.obj['name']]:
doc=db.get(row.id)
if doc['id'] != ws.obj['id']:
proclog.warning("Duplicate name {} for worksets {} and {}".format(doc['name'], doc['id'], final_doc['id']))
db.delete(doc)
db.save(final_doc)
proclog.info("updating {0}".format(ws.obj['name']))
queue.task_done()