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
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
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": ("facility_batch_id", True, None, lambda x: util.convertdata(x, int)),
"provider": ("provider", True),
"provider_catalog_id": "provider_catalog_id",
"provider_sample_id": "provider_sample_id",
"chemical_synthesis_reference": "chemical_synthesis_reference",
"purity": "purity",
"purity_method": "purity_method",
"aqueous_solubility": "aqueous_solubility",
"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),
}
# 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)
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["smallmolecule"] = 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
def main(path):
sheet_name = 'sheet 1'
start_row = 1
sheet = iu.readtable([path, sheet_name, start_row])
properties = ('model_field','required','default','converter')
column_definitions = {
'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',False),
'provider_catalog_id':'provider_catalog_id',
'provider_sample_id':'provider_batch_id',
'molecular_weight':(
'_molecular_weight',False,None,
lambda x: util.convertdata(x, float)),
'molecular_formula':'_molecular_formula',
'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),
}
column_definitions = util.fill_in_column_definitions(
properties,column_definitions)
cols = util.find_columns(column_definitions, sheet.labels,
all_sheet_columns_required=False)
rows = 0
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]
required = properties['required']
default = properties['default']
converter = properties['converter']
model_field = properties['model_field']
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))
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.exception(
'sm identifiers not found: %r, row: %d',
small_molecule_lookup,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.exception(
'Invalid smallmolecule batch initializer: %r, row: %d',
initializer, rows+start_row+2)
raise