def get_sequencing_steps(session, interval="24 hours"):
#38, 46 and 714 are hiseq, miseq and hiseqX sequencing
return get_last_modified_processes(session, [38,714,46], interval)
def get_sequencing_steps(session, interval="24 hours"):
#38, 46, 714 and 1454 are hiseq, miseq, hiseqX and novaseq sequencing
return get_last_modified_processes(session, [38,714, 1454, 46], interval)
def main(args):
log = lutils.setupLog('worksetlogger', args.logfile)
lims = Lims(BASEURI, USERNAME, PASSWORD)
#this will decide how far back we are looking
if args.ws:
wsp = Process(lims, id=args.ws)
lc = lclasses.LimsCrawler(lims, wsp)
lc.crawl()
try:
ws = lclasses.Workset(lims,lc, log)
except NameError:
log.error("no name found for this workset")
mycouch = sdb.Couch()
mycouch.set_db("worksets")
mycouch.connect()
view = mycouch.db.view('worksets/name')
#If there is already a workset with that name in the DB
if len(view[ws.obj['name']].rows) == 1:
remote_doc = view[ws.obj['name']].rows[0].value
#remove id and rev for comparison
doc_id = remote_doc.pop('_id')
doc_rev = remote_doc.pop('_rev')
if remote_doc != ws.obj:
#if they are different, though they have the same name, upload the new one
ws.obj=lutils.merge(ws.obj, remote_doc)
ws.obj['_id'] = doc_id
ws.obj['_rev'] = doc_rev
mycouch.db[doc_id] = ws.obj
log.info("updating {0}".format(ws.obj['name']))
else:
log.info("not modifying {0}".format(ws.obj['name']))
elif len(view[ws.obj['name']].rows) == 0:
#it is a new doc, upload it
mycouch.save(ws.obj)
log.info("saving {0}".format(ws.obj['name']))
else:
log.warn("more than one row with name {0} found".format(ws.obj['name']))
else:
try:
from genologics_sql.queries import get_last_modified_processes, get_processes_in_history
from genologics_sql.utils import get_session
session=get_session()
#Aggregate QC, Setup workset plate, or sequencing.
recent_processes=get_last_modified_processes(session,[8,204,38,714,46])
#Setup workset plate is 204
processes_to_update=[]
for p in recent_processes:
if p.typeid==204:
processes_to_update.append(p)
else:
processes_to_update.extend(get_processes_in_history(session, p.processid, [204]))
wsts=[]
for p in set(processes_to_update):
wsts.append(Process(lims, id=p.luid))
log.info("list compiled via the DB")
except ImportError:
starting_date= datetime.today() - timedelta(args.days)
str_date= starting_date.strftime("%Y-%m-%dT%H:%M:%SZ")
wsts = lims.get_processes(type=pc.WORKSET.values(),last_modified=str_date)
log.info("list compiled via the API")
log.info("the following processes will be updated : {0}".format(wsts))
lpar.masterProcess(args, wsts, lims, log)