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
def main(argv):
parser = make_parser()
args = parser.parse_args(argv)
log_level = getattr(logging, args.loglevel)
kwargs = {"format": LOG_FORMAT, "datefmt": LOG_DATEFMT, "level": log_level}
if args.logfile:
kwargs["filename"] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
kb = KB(driver="omero")(args.host, args.user, args.passwd)
# Load enrollments and individual (needed to build sample label and for gender field)
enrolls = []
for sl in STUDY_LABELS:
logger.debug("Loading enrollments for study %s" % sl)
enrolls.extend(kb.get_enrolled(kb.get_study(sl)))
logger.debug("Fetched %d individuals" % len(enrolls))
wells_lookup = get_wells_enrolls_lookup(enrolls, kb)
logger.debug("Loading EHR records")
ehr_records = kb.get_ehr_records("(valid == True)")
ehr_records_map = {}
for r in ehr_records:
ehr_records_map.setdefault(r["i_id"], []).append(r)
# Read plate barcodes
with open(args.plates_list) as pl_list:
barcodes = [row.strip() for row in pl_list]
# Load plate
for plate_barcode in barcodes:
logger.info("Creating datasheet for plate %s" % plate_barcode)
pl = load_plate(plate_barcode, kb)
if not pl:
logger.error("No plate with barcode %s exists, skipping it." % (plate_barcode))
continue
# Load wells for selected plate
pl_wells = get_wells_by_plate(plate_barcode, kb)
with open(os.path.join(args.out_dir, "%s_datasheet.csv" % plate_barcode), "w") as of:
writer = csv.DictWriter(of, CSV_FIELDS, delimiter="\t")
writer.writeheader()
last_slot = 0
for slot, well in sorted(pl_wells.iteritems()):
cl_record = ehr_records_map[wells_lookup[well][0].individual.id]
t1d, ms = get_affections(cl_record)
# Fill empty slots
while last_slot != slot - 1:
last_slot += 1
writer.writerow(
{
"Sample_ID": "X",
"PLATE_barcode": pl.barcode,
"PLATE_name": pl.label,
"WELL_label": get_well_label(last_slot),
"INDIVIDUAL_gender": "X",
"INDIVIDUAL_vid": "X",
"T1D_affected": "X",
"MS_affected": "X",
}
)
writer.writerow(
{
"Sample_ID": get_ichip_sample_code(wells_lookup[well], pl.barcode),
"PLATE_barcode": pl.barcode,
"PLATE_name": pl.label,
"WELL_label": well.label,
"INDIVIDUAL_gender": map_gender(wells_lookup[well][0].individual),
"INDIVIDUAL_vid": wells_lookup[well][0].individual.id,
"T1D_affected": t1d,
"MS_affected": ms,
}
)
last_slot = slot
host = args.host or vlu.ome_host()
user = args.user or vlu.ome_user()
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
kb = KB(driver='omero')(host, user, passwd)
logger.debug('Reading codes from source list')
with open(args.source_list) as f:
codes = [row.strip() for row in f.readlines()]
logger.debug('Found %d codes to discard' % len(codes))
logger.debug('Retrieving enrollments for study %s' % args.source_study)
source_enrolls = kb.get_enrolled(kb.get_study(args.source_study))
logger.debug('Retrieved %d enrollments' % len(source_enrolls))
src_st_lookup = {}
for sen in source_enrolls:
src_st_lookup[sen.studyCode] = sen
to_be_discarded = []
discard_st = kb.get_study(args.discard_study)
if discard_st is None:
logger.critical('Study with label %s not found!' % args.discard_study)
sys.exit(2)
for c in codes:
try:
src_st_lookup[c].study = discard_st
to_be_discarded.append(src_st_lookup[c])
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
kb = KB(driver='omero')(host, user, passwd)
with open(args.couples_list) as f:
reader = csv.reader(f, delimiter='\t')
couples = []
for row in reader:
couples.append((row[0], row[1]))
logger.info('%d couples are going to be swapped' % len(couples))
logger.debug('Retrieving enrollments for study %s' % args.study)
enrolls = kb.get_enrolled(kb.get_study(args.study))
logger.debug('Retrieved %d enrollments' % len(enrolls))
en_lookup = {}
for en in enrolls:
en_lookup[en.studyCode] = en
for en_code1, en_code2 in couples:
logger.info('Swapping couple %s - %s' % (en_code1, en_code2))
try:
en1 = en_lookup[en_code1]
en2 = en_lookup[en_code2]
except KeyError, ke:
logger.error('Code %s not found in study %s' % (ke, args.study))
sys.exit(2)
host = args.host or vlu.ome_host()
user = args.user or vlu.ome_user()
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
kb = KB(driver='omero')(host, user, passwd)
logger.debug('Reading codes from source list')
with open(args.source_list) as f:
codes = [row.strip() for row in f.readlines()]
logger.debug('Found %d codes to discard' % len(codes))
logger.debug('Retrieving enrollments for study %s' % args.source_study)
source_enrolls = kb.get_enrolled(kb.get_study(args.source_study))
logger.debug('Retrieved %d enrollments' % len(source_enrolls))
src_st_lookup = {}
for sen in source_enrolls:
src_st_lookup[sen.studyCode] = sen
to_be_discarded = []
discard_st = kb.get_study(args.discard_study)
if discard_st is None:
logger.critical('Study with label %s not found!' % args.discard_study)
sys.exit(2)
for c in codes:
try:
src_st_lookup[c].study = discard_st
to_be_discarded.append(src_st_lookup[c])
def main(argv):
parser = make_parser()
args = parser.parse_args(argv)
log_level = getattr(logging, args.loglevel)
kwargs = {'format': LOG_FORMAT, 'datefmt': LOG_DATEFMT, 'level': log_level}
if args.logfile:
kwargs['filename'] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
kb = KB(driver='omero')(args.host, args.user, args.passwd)
# Load enrollments and individual (needed to build sample label and for gender field)
enrolls = []
for sl in STUDY_LABELS:
logger.debug('Loading enrollments for study %s' % sl)
enrolls.extend(kb.get_enrolled(kb.get_study(sl)))
logger.debug('Fetched %d individuals' % len(enrolls))
wells_lookup = get_wells_enrolls_lookup(enrolls, kb)
logger.debug('Loading EHR records')
ehr_records = kb.get_ehr_records('(valid == True)')
ehr_records_map = {}
for r in ehr_records:
ehr_records_map.setdefault(r['i_id'], []).append(r)
# Read plate barcodes
with open(args.plates_list) as pl_list:
barcodes = [row.strip() for row in pl_list]
# Load plate
for plate_barcode in barcodes:
logger.info('Creating datasheet for plate %s' % plate_barcode)
pl = load_plate(plate_barcode, kb)
if not pl:
logger.error('No plate with barcode %s exists, skipping it.' %
(plate_barcode))
continue
# Load wells for selected plate
pl_wells = get_wells_by_plate(plate_barcode, kb)
with open(
os.path.join(args.out_dir, '%s_datasheet.csv' % plate_barcode),
'w') as of:
writer = csv.DictWriter(of, CSV_FIELDS, delimiter='\t')
writer.writeheader()
last_slot = 0
for slot, well in sorted(pl_wells.iteritems()):
cl_record = ehr_records_map[wells_lookup[well]
[0].individual.id]
t1d, ms = get_affections(cl_record)
# Fill empty slots
while (last_slot != slot - 1):
last_slot += 1
writer.writerow({
'Sample_ID': 'X',
'PLATE_barcode': pl.barcode,
'PLATE_name': pl.label,
'WELL_label': get_well_label(last_slot),
'INDIVIDUAL_gender': 'X',
'INDIVIDUAL_vid': 'X',
'T1D_affected': 'X',
'MS_affected': 'X'
})
writer.writerow({
'Sample_ID':
get_ichip_sample_code(wells_lookup[well], pl.barcode),
'PLATE_barcode':
pl.barcode,
'PLATE_name':
pl.label,
'WELL_label':
well.label,
'INDIVIDUAL_gender':
map_gender(wells_lookup[well][0].individual),
'INDIVIDUAL_vid':
wells_lookup[well][0].individual.id,
'T1D_affected':
t1d,
'MS_affected':
ms
})
last_slot = slot
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
kb = KB(driver='omero')(host, user, passwd)
with open(args.couples_list) as f:
reader = csv.reader(f, delimiter='\t')
couples = []
for row in reader:
couples.append((row[0], row[1]))
logger.info('%d couples are going to be swapped' % len(couples))
logger.debug('Retrieving enrollments for study %s' % args.study)
enrolls = kb.get_enrolled(kb.get_study(args.study))
logger.debug('Retrieved %d enrollments' % len(enrolls))
en_lookup = {}
for en in enrolls:
en_lookup[en.studyCode] = en
for en_code1, en_code2 in couples:
logger.info('Swapping couple %s - %s' % (en_code1, en_code2))
try:
en1 = en_lookup[en_code1]
en2 = en_lookup[en_code2]
except KeyError, ke:
logger.error('Code %s not found in study %s' % (ke, args.study))
sys.exit(2)
gender_map = {"MALE": kb.Gender.MALE, "FEMALE": kb.Gender.FEMALE}
by_label = {}
for label, gender, father, mother in individuals_defs:
conf = {"gender": gender_map[gender], "action": action}
if father:
conf["father"] = by_label[father]
if mother:
conf["mother"] = by_label[mother]
i = kb.factory.create(kb.Individual, conf).save()
by_label[label] = i
e = kb.factory.create(kb.Enrollment, {"study": study, "individual": i, "studyCode": label}).save()
""" ..
Note that studyCode is the code assigned to each individual in a
specific study. As a test, we now loop on all the individuals enrolled
in the study and check if they are who we think they should be.
"""
for e in kb.get_enrolled(study):
assert e.individual == by_label[e.studyCode]
""" ..
See CoreOmeroWrapper.__eq__ for details on what we actually checked
for with the == operator.
"""
