def main(args):
with open(args.conf, 'r') as conf_file:
conf = yaml.safe_load(conf_file)
couch = lutils.setupServer(conf)
with open(args.oconf, 'r') as ocf:
oconf = yaml.load(ocf)['order_portal']
mainlog = get_logger('psullogger')
lims_db = get_session()
host = get_configuration()['url']
if args.name:
pj_id = lims_db.query(
DBProject.luid).filter(DBProject.name == args.name).scalar()
else:
pj_id = args.pid
P = ProjectSQL(lims_db, mainlog, pj_id, host, couch, oconf)
if args.test:
pp = pprint.pprint(P.obj)
else:
P.save()
def main(args):
log = lutils.setupLog('bioinfologger', args.logfile)
lims = Lims(BASEURI, USERNAME, PASSWORD)
with open(args.conf) as conf_file:
conf = yaml.safe_load(conf_file)
bioinfodb = lutils.setupServer(conf)['bioinfo_analysis']
open_projects = bioinfodb.view('latest_data/sample_id_open')
for row in open_projects.rows:
project_id = row.key[0]
sample_id = row.key[3]
close_date = None
try:
close_date = Project(lims=lims, id=project_id).close_date
except HTTPError as e:
if '404: Project not found' in e.message:
log.error('Project '+project_id+' not found in LIMS')
continue
if close_date is not None:
try:
doc = bioinfodb.get(row.id)
except Exception as e:
log.error(e + 'in Project '+project_id+ ' Sample '+sample_id+ ' while accessing doc from statusdb')
doc['project_closed'] = True
try:
bioinfodb.save(doc)
log.info('Updated Project '+project_id+ ' Sample '+sample_id)
except Exception as e:
log.error(e + 'in Project '+project_id+ ' Sample '+sample_id+ ' while saving to statusdb')
def main(args):
lims_db = get_session()
lims = Lims(BASEURI, USERNAME, PASSWORD)
with open(args.conf) as cf:
db_conf = yaml.load(cf)
couch = setupServer(db_conf)
db = couch["expected_yields"]
postgres_string = "{} hours".format(args.hours)
project_ids = get_last_modified_projectids(lims_db, postgres_string)
for project in [Project(lims, id=x) for x in project_ids]:
samples_count = 0
samples = lims.get_samples(projectname=project.name)
for sample in samples:
if not ("Status (manual)" in sample.udf
and sample.udf["Status (manual)"] == "Aborted"):
samples_count += 1
try:
lanes_ordered = project.udf['Sequence units ordered (lanes)']
key = parse_sequencing_platform(project.udf['Sequencing platform'])
except:
continue
for row in db.view("yields/min_yield"):
db_key = [x.lower() if x else None for x in row.key]
if db_key == key:
try:
project.udf['Reads Min'] = float(
row.value) * lanes_ordered / samples_count
project.put()
except ZeroDivisionError:
pass
def main(args):
with open(args.conf) as conf_file:
conf = yaml.safe_load(conf_file)
couch = lutils.setupServer(conf)
mainlog = get_logger('fsullogger')
db_session = get_session()
query = "select distinct pro.* from container ct \
inner join containerplacement cp on ct.containerid=cp.containerid \
inner join processiotracker piot on piot.inputartifactid=cp.processartifactid \
inner join process pro on pro.processid=piot.processid \
where pro.typeid in ({seq_type_ids}) and ct.name='{ct_name}';".format(
seq_type_ids=",".join(list(pc_cg.SEQUENCING.keys())),
ct_name=args.flowcell)
seq_steps = db_session.query(Process).from_statement(text(query)).all()
for step in seq_steps:
for udf in step.udfs:
if udf.udfname == "Run ID":
fcid = udf.udfvalue
# generate the lims_data dict key
lims_data = create_lims_data_obj(db_session, step)
if args.test:
pp = pprint.pprint(lims_data)
else:
mainlog.info("updating {}".format(fcid))
# update the couch right couch document
upload_to_couch(couch, fcid, lims_data)
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(args):
lims_db = get_session()
lims = Lims(BASEURI,USERNAME,PASSWORD)
with open(args.conf) as cf:
db_conf = yaml.load(cf)
couch = setupServer(db_conf)
db = couch["expected_yields"]
postgres_string="{} hours".format(args.hours)
project_ids=get_last_modified_projectids(lims_db, postgres_string)
for project in [Project(lims, id=x) for x in project_ids]:
samples_count = 0
samples = lims.get_samples(projectname=project.name)
for sample in samples:
if not("Status (manual)" in sample.udf and sample.udf["Status (manual)"] == "Aborted"):
samples_count +=1
try:
lanes_ordered = project.udf['Sequence units ordered (lanes)']
key = parse_sequencing_platform(project.udf['Sequencing platform'])
except:
continue
for row in db.view("yields/min_yield"):
db_key = [x.lower() if x else None for x in row.key]
if db_key==key:
try:
project.udf['Reads Min'] = float(row.value) * lanes_ordered / samples_count
project.put()
except ZeroDivisionError:
pass
def main(args):
#get the session with the lims db
db_session=get_session()
#set up a log
mainlog = logging.getLogger('fsullogger')
mainlog.setLevel(level=logging.INFO)
mfh = logging.handlers.RotatingFileHandler(args.logfile, maxBytes=209715200, backupCount=5)
mft = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
mfh.setFormatter(mft)
mainlog.addHandler(mfh)
#read the configuration
with open(args.conf) as conf_file:
conf=yaml.load(conf_file)
couch=setupServer(conf)
interval="{} hours".format(args.hours)
#list the right sequencing steps
seq_steps=get_sequencing_steps(db_session, interval)
for step in seq_steps:
for udf in step.udfs:
if udf.udfname=="Run ID":
fcid=udf.udfvalue
mainlog.info("updating {}".format(fcid))
#generate the lims_data dict key
lims_data=create_lims_data_obj(db_session, step)
#update the couch right couch document
upload_to_couch(couch,fcid, lims_data)
def main(args):
#get the session with the lims db
db_session = get_session()
#set up a log
mainlog = logging.getLogger('fsullogger')
mainlog.setLevel(level=logging.INFO)
mfh = logging.handlers.RotatingFileHandler(args.logfile,
maxBytes=209715200,
backupCount=5)
mft = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
mfh.setFormatter(mft)
mainlog.addHandler(mfh)
#read the configuration
with open(args.conf) as conf_file:
conf = yaml.load(conf_file, Loader=yaml.SafeLoader)
couch = setupServer(conf)
interval = "{} hours".format(args.hours)
#list the right sequencing steps
if args.flowcell:
query = "select distinct pro.* from container ct \
inner join containerplacement cp on ct.containerid=cp.containerid \
inner join processiotracker piot on piot.inputartifactid=cp.processartifactid \
inner join process pro on pro.processid=piot.processid \
where pro.typeid in ({seq_type_ids}) and ct.name='{ct_name}';".format(
seq_type_ids=",".join(list(pc_cg.SEQUENCING.keys())),
ct_name=args.flowcell)
seq_steps = db_session.query(Process).from_statement(text(query)).all()
else:
seq_steps = get_sequencing_steps(db_session, interval)
for step in seq_steps:
for udf in step.udfs:
if udf.udfname == "Run ID":
fcid = udf.udfvalue
mainlog.info("updating {}".format(fcid))
#generate the lims_data dict key
lims_data = create_lims_data_obj(db_session, step)
#update the couch right couch document
upload_to_couch(couch, fcid, lims_data)
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):
with open(args.conf, 'r') as conf_file:
conf = yaml.safe_load(conf_file)
couch = lutils.setupServer(conf)
db = couch['projects']
view = db.view('samples/customer_names')
d = None
for row in view[args.project]:
d = row.value
if not d:
print("Project not found")
return 0
print('<table class="table table-striped">')
print('<tr><th>NGI Name</th><th>Customer Name</th></tr>')
for sample in sorted(d.keys()):
print("<tr><td>{}</td><td>{}</td></tr>".format(sample, d[sample]))
print("</table>")