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 processWSUL(options, queue, logqueue):
mycouch = sdb.Couch()
mycouch.set_db("worksets")
mycouch.connect()
view = mycouch.db.view('worksets/name')
mylims = Lims(BASEURI, USERNAME, PASSWORD)
work=True
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:
wsp = Process(mylims, id=ws_id)
if not wsp.date_run:
continue
lc = lclasses.LimsCrawler(mylims, wsp)
lc.crawl()
try:
ws = lclasses.Workset(mylims,lc, proclog)
except NameError:
continue
#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
proclog.info("updating {0}".format(ws.obj['name']))
else:
proclog.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)
proclog.info("saving {0}".format(ws.obj['name']))
else:
proclog.warn("more than one row with name {0} found".format(ws.obj['name']))
#signals to queue job is done
queue.task_done()
def processWSUL(options, queue, logqueue):
mycouch = sdb.Couch()
mycouch.set_db("worksets")
mycouch.connect()
view = mycouch.db.view('worksets/name')
mylims = Lims(BASEURI, USERNAME, PASSWORD)
work=True
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:
wsp = Process(mylims, id=ws_id)
if not wsp.date_run:
continue
lc = lclasses.LimsCrawler(mylims, wsp)
lc.crawl()
try:
ws = lclasses.Workset(mylims,lc, proclog)
except NameError:
continue
#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
proclog.info("updating {0}".format(ws.obj['name']))
else:
proclog.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)
proclog.info("saving {0}".format(ws.obj['name']))
else:
proclog.warn("more than one row with name {0} found".format(ws.obj['name']))
#signals to queue job is done
queue.task_done()
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")
#pprint(ws.obj)
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:
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("the following processes will be updated : {0}".format(wsts))
lpar.masterProcess(args, wsts, lims, log)
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()
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)
