def add_chips():
from iondb.utils.default_chip_args import default_chip_args
'''Sets the per chip default analysis args into the
`chips` table in the database. '''
try:
# Determine slots by number of cpu sockets installed
p1 = subprocess.Popen("/usr/bin/lscpu",stdout=subprocess.PIPE)
p2 = subprocess.Popen(["grep","^CPU socket"],stdin=p1.stdout,stdout=subprocess.PIPE)
sockets = p2.stdout.read().strip().split(":")[1]
sockets = int(sockets)
except:
sockets = 2
print traceback.format_exc()
chips = (('318',1,'318'),
('316',1,'316'),
('314',1,'314'),
('900',1,'PI'),
)
for (name,slots,description) in chips:
# get default args for this chip
args = default_chip_args(name)
try:
# (this case when updating TS typically)
c = models.Chip.objects.get(name=name)
c.slots = slots
c.analysisargs = args['analysisArgs']
c.basecallerargs = args['basecallerArgs']
c.beadfindargs = args['beadfindArgs']
c.thumbnailanalysisargs = args['thumbnailAnalysisArgs']
c.thumbnailbasecallerargs = args['thumbnailBasecallerArgs']
c.thumbnailbeadfindargs = args['thumbnailBeadfindArgs']
c.save()
except ObjectDoesNotExist:
# (this case is only on TS initialization or when new chips added)
c = models.Chip(name=name,
slots=slots,
description = description,
analysisargs = args['analysisArgs'],
basecallerargs = args['basecallerArgs'],
beadfindargs = args['beadfindArgs'],
thumbnailanalysisargs = args['thumbnailAnalysisArgs'],
thumbnailbasecallerargs = args['thumbnailBasecallerArgs'],
thumbnailbeadfindargs = args['thumbnailBeadfindArgs']
)
c.save()
print "Added Chip object named %s." % name
# Remove the special chip labelled 'takeover'; no longer used.
try:
c = models.Chip.objects.get(name='takeover')
c.delete()
print "Deleted Chip object named 'takeover'"
except:
pass
return
def add_chips_obsolete():
from iondb.utils.default_chip_args import default_chip_args
'''Sets the per chip default analysis args into the `chips` table in the database. '''
chips = (('314','314'),
('316','316'),
('318','318'),
('318v2','318v2'),
('316v2','316v2'),
('314v2','314v2'),
('P1.0.19','P0'),
('900','P1'),
('900v2','P1v2'),
('P1.1.16','P1'),
('P1.1.17','P1'),
('P1.2.18','P1'),
('P2.0.16','P2'),
('P2.1.16','P2'),
('P2.2.16','P2'),
)
for (name,description) in chips:
# get default args for this chip
args = default_chip_args(name)
try:
# (this case when updating TS typically)
c = models.Chip.objects.get(name=name)
c.slots = args['slots']
c.beadfindargs = args['beadfindArgs']
c.analysisargs = args['analysisArgs']
c.prebasecallerargs = args['prebasecallerArgs']
c.basecallerargs = args['basecallerArgs']
c.thumbnailbeadfindargs = args['thumbnailBeadfindArgs']
c.thumbnailanalysisargs = args['thumbnailAnalysisArgs']
c.prethumbnailbasecallerargs = args['prethumbnailBasecallerArgs']
c.thumbnailbasecallerargs = args['thumbnailBasecallerArgs']
c.save()
except ObjectDoesNotExist:
# (this case is only on TS initialization or when new chips added)
c = models.Chip(name=name,
slots=args['slots'],
description = description,
analysisargs = args['analysisArgs'],
basecallerargs = args['basecallerArgs'],
beadfindargs = args['beadfindArgs'],
thumbnailanalysisargs = args['thumbnailAnalysisArgs'],
thumbnailbasecallerargs = args['thumbnailBasecallerArgs'],
thumbnailbeadfindargs = args['thumbnailBeadfindArgs']
)
c.save()
print "Added Chip object named %s." % name
# Remove the special chip labelled 'takeover'; no longer used.
try:
c = models.Chip.objects.get(name='takeover')
c.delete()
print "Deleted Chip object named 'takeover'"
except:
pass
return
def add_chips_obsolete():
from iondb.utils.default_chip_args import default_chip_args
'''Sets the per chip default analysis args into the `chips` table in the database. '''
chips = (
('314', '314'),
('316', '316'),
('318', '318'),
('318v2', '318v2'),
('316v2', '316v2'),
('314v2', '314v2'),
('P1.0.19', 'P0'),
('900', 'P1'),
('900v2', 'P1v2'),
('P1.1.16', 'P1'),
('P1.1.17', 'P1'),
('P1.2.18', 'P1'),
('P2.0.16', 'P2'),
('P2.1.16', 'P2'),
('P2.2.16', 'P2'),
)
for (name, description) in chips:
# get default args for this chip
args = default_chip_args(name)
try:
# (this case when updating TS typically)
c = models.Chip.objects.get(name=name)
c.slots = args['slots']
c.beadfindargs = args['beadfindArgs']
c.analysisargs = args['analysisArgs']
c.prebasecallerargs = args['prebasecallerArgs']
c.basecallerargs = args['basecallerArgs']
c.thumbnailbeadfindargs = args['thumbnailBeadfindArgs']
c.thumbnailanalysisargs = args['thumbnailAnalysisArgs']
c.prethumbnailbasecallerargs = args['prethumbnailBasecallerArgs']
c.thumbnailbasecallerargs = args['thumbnailBasecallerArgs']
c.save()
except ObjectDoesNotExist:
# (this case is only on TS initialization or when new chips added)
c = models.Chip(
name=name,
slots=args['slots'],
description=description,
analysisargs=args['analysisArgs'],
basecallerargs=args['basecallerArgs'],
beadfindargs=args['beadfindArgs'],
thumbnailanalysisargs=args['thumbnailAnalysisArgs'],
thumbnailbasecallerargs=args['thumbnailBasecallerArgs'],
thumbnailbeadfindargs=args['thumbnailBeadfindArgs'])
c.save()
print "Added Chip object named %s." % name
# Remove the special chip labelled 'takeover'; no longer used.
try:
c = models.Chip.objects.get(name='takeover')
c.delete()
print "Deleted Chip object named 'takeover'"
except:
pass
return
def add_chips_obsolete():
from iondb.utils.default_chip_args import default_chip_args
"""Sets the per chip default analysis args into the `chips` table in the database. """
chips = (
("314", "314"),
("316", "316"),
("318", "318"),
("318v2", "318v2"),
("316v2", "316v2"),
("314v2", "314v2"),
("P1.0.19", "P0"),
("900", "P1"),
("900v2", "P1v2"),
("P1.1.16", "P1"),
("P1.1.17", "P1"),
("P1.2.18", "P1"),
("P2.0.16", "P2"),
("P2.1.16", "P2"),
("P2.2.16", "P2"),
)
for (name, description) in chips:
# get default args for this chip
args = default_chip_args(name)
try:
# (this case when updating TS typically)
c = models.Chip.objects.get(name=name)
c.slots = args["slots"]
c.beadfindargs = args["beadfindArgs"]
c.analysisargs = args["analysisArgs"]
c.prebasecallerargs = args["prebasecallerArgs"]
c.basecallerargs = args["basecallerArgs"]
c.thumbnailbeadfindargs = args["thumbnailBeadfindArgs"]
c.thumbnailanalysisargs = args["thumbnailAnalysisArgs"]
c.prethumbnailbasecallerargs = args["prethumbnailBasecallerArgs"]
c.thumbnailbasecallerargs = args["thumbnailBasecallerArgs"]
c.save()
except ObjectDoesNotExist:
# (this case is only on TS initialization or when new chips added)
c = models.Chip(
name=name,
slots=args["slots"],
description=description,
analysisargs=args["analysisArgs"],
basecallerargs=args["basecallerArgs"],
beadfindargs=args["beadfindArgs"],
thumbnailanalysisargs=args["thumbnailAnalysisArgs"],
thumbnailbasecallerargs=args["thumbnailBasecallerArgs"],
thumbnailbeadfindargs=args["thumbnailBeadfindArgs"],
)
c.save()
print("Added Chip object named %s." % name)
# Remove the special chip labelled 'takeover'; no longer used.
try:
c = models.Chip.objects.get(name="takeover")
c.delete()
print("Deleted Chip object named 'takeover'")
except Exception:
pass
return
