class App(object):
def __init__(self, host, user, passwd,
study_label,
maker, model, release):
self.kb = KB(driver='omero')(host, user, passwd)
self.mset = self.kb.get_snp_markers_set(maker, model, release)
self.logger = logging.getLogger()
if not self.mset:
raise ValueError('SNPMarkersSet[%s,%s,%s] has not been defined.'
% (maker, model, release))
#--
alabel = 'load_genotypes-setup-%s' % time.time()
self.asetup = self.kb.factory.create(self.kb.ActionSetup,
{'label' : alabel,
'conf' : ''}).save()
#--
dmaker, dmodel, drelease = 'CRS4', 'load_genotypes', '0.1'
dlabel = '%s-%s-%s' % (dmaker, dmodel, drelease)
device = self.kb.get_device(dlabel)
if not device:
device = self.kb.factory.create(self.kb.Device,
{'label' : dlabel,
'maker' : dmaker,
'model' : dmodel,
'release' : drelease}).save()
self.device = device
#-- FIXME this will break if study is not defined.
self.study = self.kb.get_study(study_label)
def check_snp_markers_set(self, marker_types, marker_names):
self.logger.info('start checking snp_markers_set')
mdefs, msetc = self.kb.get_snp_markers_set_content(self.mset)
rs_labels = mdefs['rs_label']
for t, n in it.izip(marker_types, marker_names):
if t == 'M':
if not n in rs_labels:
msg = 'marker %s is not in the specified SNPMarkersSet' % n
self.logger.critical(msg)
raise ValueError(msg)
self.logger.info('done checking snp_markers_set')
def create_action(self, target):
conf = {'setup' : self.asetup,
'device' : self.device,
'actionCategory' : self.kb.ActionCategory.MEASUREMENT,
'operator' : 'Alfred E. Neumann',
'context' : self.study,
'target' : target,
}
action = self.kb.factory.create(self.kb.ActionOnVessel, conf).save()
return action
def create_data_sample(self, action, label):
conf = {'snpMarkersSet' : self.mset,
'label' : label,
'status' : self.kb.DataSampleStatus.USABLE,
'action' : action}
return self.kb.factory.create(self.kb.GenotypeDataSample, conf).save()
def load(self, pedfile, datfile, conf_value=1.0):
pr = PedReader(pedfile, datfile, conf_value)
self.check_snp_markers_set(pr.marker_types, pr.marker_names)
#--
self.logger.info('start loading from pedfile %s' % pedfile.name)
for x in pr:
sample = self.kb.get_vessel(x['sample_label'])
if not sample:
self.logger.error('No sample with label %s in VL' % x['sample_label'])
continue
action = self.create_action(sample)
avid = action.id
action.unload()
data_sample = self.create_data_sample(action, x['label'])
data_object = self.kb.add_gdo_data_object(avid, data_sample,
x['probs'], x['confs'])
self.logger.info('-- loaded %s' % x['label'])
self.logger.info('done loading from pedfile %s' % pedfile.name)
class App(object):
def __init__(self, host, user, passwd, study_label, maker, model, release):
self.kb = KB(driver='omero')(host, user, passwd)
self.mset = self.kb.get_snp_markers_set(maker, model, release)
self.logger = logging.getLogger()
if not self.mset:
raise ValueError('SNPMarkersSet[%s,%s,%s] has not been defined.' %
(maker, model, release))
#--
alabel = 'load_genotypes-setup-%s' % time.time()
self.asetup = self.kb.factory.create(self.kb.ActionSetup, {
'label': alabel,
'conf': ''
}).save()
#--
dmaker, dmodel, drelease = 'CRS4', 'load_genotypes', '0.1'
dlabel = '%s-%s-%s' % (dmaker, dmodel, drelease)
device = self.kb.get_device(dlabel)
if not device:
device = self.kb.factory.create(
self.kb.Device, {
'label': dlabel,
'maker': dmaker,
'model': dmodel,
'release': drelease
}).save()
self.device = device
#-- FIXME this will break if study is not defined.
self.study = self.kb.get_study(study_label)
def check_snp_markers_set(self, marker_types, marker_names):
self.logger.info('start checking snp_markers_set')
mdefs, msetc = self.kb.get_snp_markers_set_content(self.mset)
rs_labels = mdefs['rs_label']
for t, n in it.izip(marker_types, marker_names):
if t == 'M':
if not n in rs_labels:
msg = 'marker %s is not in the specified SNPMarkersSet' % n
self.logger.critical(msg)
raise ValueError(msg)
self.logger.info('done checking snp_markers_set')
def create_action(self, target):
conf = {
'setup': self.asetup,
'device': self.device,
'actionCategory': self.kb.ActionCategory.MEASUREMENT,
'operator': 'Alfred E. Neumann',
'context': self.study,
'target': target,
}
action = self.kb.factory.create(self.kb.ActionOnVessel, conf).save()
return action
def create_data_sample(self, action, label):
conf = {
'snpMarkersSet': self.mset,
'label': label,
'status': self.kb.DataSampleStatus.USABLE,
'action': action
}
return self.kb.factory.create(self.kb.GenotypeDataSample, conf).save()
def load(self, pedfile, datfile, conf_value=1.0):
pr = PedReader(pedfile, datfile, conf_value)
self.check_snp_markers_set(pr.marker_types, pr.marker_names)
#--
self.logger.info('start loading from pedfile %s' % pedfile.name)
for x in pr:
sample = self.kb.get_vessel(x['sample_label'])
if not sample:
self.logger.error('No sample with label %s in VL' %
x['sample_label'])
continue
action = self.create_action(sample)
avid = action.id
action.unload()
data_sample = self.create_data_sample(action, x['label'])
data_object = self.kb.add_gdo_data_object(avid, data_sample,
x['probs'], x['confs'])
self.logger.info('-- loaded %s' % x['label'])
self.logger.info('done loading from pedfile %s' % pedfile.name)
