class VidMapper(object):
def __init__(self, host, user, passwd, logger, study):
self.logger = logger
self.study = study
self.kb = KB(driver="omero")(host, user, passwd)
plates = self.kb.get_objects(self.kb.TiterPlate)
self.logger.info("fetched %d plates" % len(plates))
self.plate_map = {}
self.enroll_map = {}
for p in plates:
self.plate_map[p.omero_id] = p.barcode
s = self.kb.get_study(self.study)
enrolls = self.kb.get_enrolled(s)
self.logger.info("fetched %d enrollments" % len(enrolls))
for e in enrolls:
self.logger.debug('Retrieving wells for %s' % e.studyCode)
wells = [
w for w in self.kb.get_vessels_by_individual(
e.individual, "PlateWell")
]
self.enroll_map[e.studyCode] = wells
def map_vid(self, r):
en_code = r["source"]
pl_barcode = en_code.split("|")[1]
try:
wells = self.enroll_map[en_code]
except KeyError:
msg = "%s is not enrolled in %s" % (en_code, self.study)
self.logger.error(msg)
raise ValueError(msg)
self.logger.info("found %d wells for %s" % (len(wells), en_code))
imm_wells = [
w for w in wells
if self.plate_map[w.container.omero_id] == pl_barcode
]
if len(imm_wells) > 1:
msg = ("more than 1 (%d) immuno wells for plate %s" %
(len(imm_wells), pl_barcode))
self.logger.error(msg)
raise ValueError(msg)
elif len(imm_wells) == 0:
msg = "no immuno well for plate %s" % pl_barcode
self.logger.warn(msg)
raise ValueError(msg)
else:
r["source"] = imm_wells[0].id
class VidMapper(object):
def __init__(self, host, user, passwd, logger, study):
self.logger = logger
self.study = study
self.kb = KB(driver="omero")(host, user, passwd)
plates = self.kb.get_objects(self.kb.TiterPlate)
self.logger.info("fetched %d plates" % len(plates))
self.plate_map = {}
self.enroll_map = {}
for p in plates:
self.plate_map[p.omero_id] = p.barcode
s = self.kb.get_study(self.study)
enrolls = self.kb.get_enrolled(s)
self.logger.info("fetched %d enrollments" % len(enrolls))
for e in enrolls:
self.logger.debug("Retrieving wells for %s" % e.studyCode)
wells = [w for w in self.kb.get_vessels_by_individual(e.individual, "PlateWell")]
self.enroll_map[e.studyCode] = wells
def map_vid(self, r):
en_code = r["source"]
pl_barcode = en_code.split("|")[1]
try:
wells = self.enroll_map[en_code]
except KeyError:
msg = "%s is not enrolled in %s" % (en_code, self.study)
self.logger.error(msg)
raise ValueError(msg)
self.logger.info("found %d wells for %s" % (len(wells), en_code))
imm_wells = [w for w in wells if self.plate_map[w.container.omero_id] == pl_barcode]
if len(imm_wells) > 1:
msg = "more than 1 (%d) immuno wells for plate %s" % (len(imm_wells), pl_barcode)
self.logger.error(msg)
raise ValueError(msg)
elif len(imm_wells) == 0:
msg = "no immuno well for plate %s" % pl_barcode
self.logger.warn(msg)
raise ValueError(msg)
else:
r["source"] = imm_wells[0].id
