if (facilityId <= 30000): # SM or Screen
logger.info('look for the small molecule for:' + str(facilityId))
saltId = util.int_converter(args.saltId)
if (saltId is not None):
logger.info('look for the small molecule for saltId ' +
str(saltId))
try:
sm = SmallMolecule(facility_id=facilityId, salt_id=saltId)
attachedFile.salt_id_for = saltId
batchId = util.int_converter(args.batchId)
if (batchId is not None):
logger.info('look for the batch Id: ' + str(batchId))
attachedFile.batch_id_for = batchId
try:
smb = SmallMoleculeBatch(smallmolecule=sm,
facility_batch_id=batchId)
except ObjectDoesNotExist, e:
logger.error(
str(('No such SmallMoleculeBatch found',
facilityId, saltId, batchId, e)))
raise e
except ObjectDoesNotExist, e:
logger.error(
str(('No such SmallMolecule found', facilityId, saltId,
e)))
raise e
else: # it's a screen/dataset
try:
ds = DataSet.objects.get(facility_id=facilityId)
except ObjectDoesNotExist, e:
def main(path):
"""
Read in the smallmolecule batch info
"""
sheet_name = 'sheet 1'
start_row = 1
sheet = iu.readtable([path, sheet_name, start_row
]) # Note, skipping the header row by default
properties = ('model_field', 'required', 'default', 'converter')
column_definitions = {
# NOTE: even though these db field are not integers,
# it is convenient to convert the read in values to INT to make sure they are not interpreted as float values
'facility_id':
('facility_id', True, None, lambda x: util.convertdata(x, int)),
'salt_id': ('salt_id', True, None, lambda x: util.convertdata(x, int)),
'facility_batch_id':
('batch_id', True, None, lambda x: util.convertdata(x, int)),
'provider': ('provider_name', True),
'provider_catalog_id':
'provider_catalog_id',
'provider_sample_id':
'provider_batch_id',
'chemical_synthesis_reference':
'chemical_synthesis_reference',
'purity':
'purity',
'purity_method':
'purity_method',
'aqueous_solubility':
'aqueous_solubility',
# FIXME: should warn the user if no unit is provided when
# aqueous_solubility is provided
'aqueous_solubility_unit':
'aqueous_solubility_unit',
'Date Data Received':
('date_data_received', False, None, util.date_converter),
'Date Loaded': ('date_loaded', False, None, util.date_converter),
'Date Publicly Available':
('date_publicly_available', False, None, util.date_converter),
'Most Recent Update': ('date_updated', False, None,
util.date_converter),
}
# convert the labels to fleshed out dict's, with strategies for optional, default and converter
column_definitions = util.fill_in_column_definitions(
properties, column_definitions)
# create a dict mapping the column ordinal to the proper column definition dict
cols = util.find_columns(column_definitions,
sheet.labels,
all_sheet_columns_required=False)
rows = 0
logger.debug(str(('cols: ', cols)))
for row in sheet:
r = util.make_row(row)
initializer = {}
small_molecule_lookup = {'facility_id': None, 'salt_id': None}
for i, value in enumerate(r):
if i not in cols: continue
properties = cols[i]
logger.debug(str(('read col: ', i, ', ', properties)))
required = properties['required']
default = properties['default']
converter = properties['converter']
model_field = properties['model_field']
# Todo, refactor to a method
logger.debug(str(('raw value', value)))
if (converter != None):
value = converter(value)
if (value == None):
if (default != None):
value = default
if (value == None and required == True):
raise Exception('Field is required: %s, record: %d' %
(properties['column_label'], rows))
logger.debug(
str(('model_field: ', model_field, ', value: ', value)))
if (model_field in small_molecule_lookup):
small_molecule_lookup[model_field] = value
if (None not in small_molecule_lookup.values()):
try:
sm = SmallMolecule.objects.get(**small_molecule_lookup)
initializer['reagent'] = sm
except Exception, e:
logger.error(
str(('sm identifiers not found',
small_molecule_lookup, 'row',
rows + start_row + 2)))
raise
else:
initializer[model_field] = value
try:
logger.debug(str(('initializer: ', initializer)))
smb = SmallMoleculeBatch(**initializer)
smb.save()
logger.debug(str(('smb created:', smb)))
rows += 1
except Exception, e:
logger.error(
str(("Invalid smallmolecule batch initializer: ", initializer,
'row', rows + start_row + 2, e)))
raise
