if(dataRecord.control_type is not None and
dataRecord.smallmolecule is not None):
raise Exception(str((
'Cannot define a control type for a non-control well '
'(well mapped to a small molecule batch)',
dataRecord.smallmolecule,dataRecord.control_type,
'row',current_row)))
if metaColumnDict['batch_id'] > -1:
temp = util.convertdata(r[metaColumnDict['batch_id']], int)
if(temp != None):
if(dataRecord.batch_id is not None and
temp is not None and dataRecord.batch_id != temp):
raise Exception(str((
'batch id field(1) does not match batch id set with '
'entity(2):',temp,dataRecord.batch_id)))
dataRecord.batch_id = temp
#dataRecord.save()
logger.debug(str(('datarecord created:', dataRecord)))
datapoint_batch = []
for i,value in enumerate(r):
# NOTE: shall there be an "empty" datapoint?
# No, since non-existance of data in the worksheet does not mean
# "null" will mean "no value entered"
# TODO: verify/read existing code, ask Dave
if(value.strip()==''): continue
if i in dataColumnList:
dataColumn = dataColumnList[i]
dataPoint = _create_datapoint(dataColumn, dataset, dataRecord, value)
#dataPoint.save()
datapoint_batch.append(dataPoint)
if(map_column > -1):
try:
value = util.convertdata(r[map_column].strip())
if(value != None and value != '' ):
value = value.split("-")
if len(value) < 2: raise Exception('Small Molecule (Batch) format is #####-###(-#) **Note that (batch) is optional')
x = value[0]
facility = util.convertdata(x,int)
salt = value[1]
try:
dataRecord.smallmolecule = SmallMolecule.objects.get(facility_id=facility, salt_id=salt)
except Exception, e:
logger.error(str(('could not locate small molecule:', facility)))
raise
if(len(value)>2):
dataRecord.batch_id = util.convertdata(value[2],int)
# TODO: validate that the batch exists? (would need to do for all types, not just Small Molecule
mapped = True
except Exception, e:
logger.error(str(("Invalid Small Molecule (or batch) identifiers: ", value, e,'row',current_row)))
raise
map_column = mappingColumnDict['Plate']
if(map_column > -1):
try:
plate_id=None
well_id=None
value = util.convertdata(r[map_column].strip())
if(value != None and value != '' ):
plate_id = util.convertdata(value,int)
value = util.convertdata(r[map_column+1].strip())