def test_create_small_molecule(self):
"""
Tests that we can create a small molecule entity.
"""
facilityId = "HMSL10001"
sm = SmallMolecule(facility_id=facilityId)
sm.save()
print "New ID: %d" % sm.id
self.assertTrue(sm.id is not None, "No ID was assigned")
sm2 = SmallMolecule.objects.get(pk=sm.id)
self.assertTrue(sm2 is not None, "Couldn't find the object")
self.assertTrue(sm2.facility_id == facilityId)
print "Created the Small Molecule: ", sm
def test_create_small_molecule(self):
"""
Tests that we can create a small molecule entity.
"""
facilityId = "HMSL10001"
sm = SmallMolecule(facility_id=facilityId)
sm.save()
print "New ID: %d" % sm.id
self.assertTrue(sm.id is not None, "No ID was assigned")
sm2 = SmallMolecule.objects.get(pk=sm.id)
self.assertTrue(sm2 is not None, "Couldn't find the object")
self.assertTrue(sm2.facility_id == facilityId)
print "Created the Small Molecule: ", sm
def test_create_multiple_small_molecules(self):
"""
Tests that we can create a few small molecule objects in the db, and select a subset
"""
facilityIdBase = "HMSL"
for x in range(100) :
sm = SmallMolecule(facility_id=facilityIdBase + str(10000+x),pub_date=timezone.now())
sm.save()
self.assertEqual(100, SmallMolecule.objects.all().count(), "Should be 100 items, but was %d" % SmallMolecule.objects.all().count())
# read back a small sample
resultSet = SmallMolecule.objects.filter(id__lt=50)
self.assertEquals(resultSet.count(), 49, "Actual size of subqery return is %d" % resultSet.count())
for y in resultSet :
print "Small Molecule: id: %d, facilityId: %s, pubDate: %s" % ( y.id, y.facility_id, y.pub_date )
def test_create_small_molecule(self):
"""
Tests that we can create a small molecule entity.
"""
facilityId = "HMSL10001"
pubDate = timezone.now()
sm = SmallMolecule(facility_id=facilityId,pub_date=pubDate)
sm.save()
print "New ID: %d" % sm.id
self.assertTrue(sm.id is not None, "No ID was assigned")
id = sm.id
sm2 = SmallMolecule.objects.get(pk=id)
self.assertTrue(sm is not None, "Couldn't find the object")
self.assertTrue(sm.facility_id == facilityId)
self.assertTrue(sm.pub_date == pubDate)
print "Created the Small Molecule: id: %d, facilityId: %s, pubDate: %s" % ( sm.id, sm.facility_id, sm.pub_date )
def build_schema(self):
schema = super(SmallMoleculeResource,self).build_schema()
schema['fields'] = get_detail_schema(SmallMolecule(),['smallmolecule'])
return schema
def main(path):
"""
Read in the sdf file
"""
# map field labels to model fields
properties = ('model_field','required','default','converter')
get_primary_name = lambda x: x.split(';')[0].strip()
get_alternate_names = lambda x: ';'.join([x.strip() for x in x.split(';')[1:]])
labels = { s2p.MOLDATAKEY:('molfile',True),
# 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_reagent_id': ('facility_id',True,None, lambda x: util.convertdata(x[x.index('HMSL')+4:],int)),
'salt_id': ('salt_id',True,None, lambda x: util.convertdata(x,int)),
'lincs_id':('lincs_id',False), #None,lambda x:util.convertdata(x,int)),
'chemical_name':('name',True),
'alternative_names':'alternative_names',
'pubchem_cid':'pubchem_cid',
'chembl_id':'chembl_id',
'chebi_id':'chebi_id',
'inchi':'_inchi',
'inchi_key':'_inchi_key',
'smiles': ('_smiles',True),
'molecular_mass':('_molecular_mass',False,None, lambda x: round(util.convertdata(x, float),2)),
'molecular_formula':'_molecular_formula',
'software':'software',
# 'concentration':'concentration',
#'well_type':('well_type',False,'experimental'),
'is_restricted':('is_restricted',False,False,util.bool_converter)}
# convert the labels to fleshed out dict's, with strategies for optional, default and converter
labels = util.fill_in_column_definitions(properties,labels)
assert typecheck.isstring(path)
with open(path) as fh:
data = fh.read().decode(DEFAULT_ENCODING)
records = s2p.parse_sdf(data)
logger.info(str(('read rows: ', len(records))))
count = 0
for record in records:
logger.debug(str(('record', record)))
initializer = {}
for key,properties in labels.items():
logger.debug(str(('look for key: ', key, ', properties: ', properties)))
required = properties['required']
default = properties['default']
converter = properties['converter']
model_field = properties['model_field']
value = record.get(key)
# Todo, refactor to a method
try:
logger.debug(str(('raw value', value)))
if(converter != None):
value = converter(value)
if(value == None ):
if( default != None ):
value = default
if(value == 'n/a'): value = None
if(value == None and required == True):
raise Exception(str(('Field is required: ', key, initializer, 'record:', count)))
logger.debug(str(('model_field: ' , model_field, ', value: ', value)))
initializer[model_field] = value
except Exception, e:
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
logger.error(str((exc_type, fname, exc_tb.tb_lineno)))
logger.error(str(('invalid input', e, 'count', count)))
raise e
# follows is a kludge, to split up the entered "chemical_name" field, on ';' - TODO: just have two fields that get entered
if(initializer['name']):
initializer['alternative_names']=get_alternate_names(initializer['name'])
initializer['name']=get_primary_name(initializer['name'])
if(logger.isEnabledFor(logging.DEBUG)): logger.debug(str(('initializer: ', initializer)))
try:
sm = SmallMolecule(**initializer)
sm.save()
logger.info(str(('sm created:', sm)))
count += 1
except Exception, e:
logger.error(str(('save failed for: ', initializer, 'error',e, 'count: ', count)))
raise e
filename = path.basename(inputFile)
attachedFile = AttachedFile(filename=filename,
facility_id_for=facilityId,
relative_path=relativePath,
is_restricted=args.isRestricted)
# lookup the Entity
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(
def main(path):
properties = ('model_field','required','default','converter')
get_primary_name = lambda x: x.split(';')[0].strip()
get_alternate_names = (
lambda x: '; '.join([x.strip() for x in x.split(';')[1:]]))
labels = { s2p.MOLDATAKEY:('molfile',True),
'facility_reagent_id': (
'facility_id',True,None,
lambda x: util.convertdata(x[x.index('HMSL')+4:],int)),
'salt_id': ('salt_id',True,None, lambda x: util.convertdata(x,int)),
'lincs_id':('lincs_id',False),
'chemical_name':('name',True),
'alternative_names':'alternative_names',
'pubchem_cid':'pubchem_cid',
'chembl_id':'chembl_id',
'chebi_id':'chebi_id',
'inchi':'_inchi',
'inchi_key':'_inchi_key',
'smiles': ('_smiles',False),
'molecular_mass':(
'_molecular_mass',False,None,
lambda x: round(util.convertdata(x, float),2)),
'relevant_citations': '_relevant_citations',
'molecular_formula':'_molecular_formula',
'software':'software',
'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),
'date_updated': ('date_updated',False,None,util.date_converter),
'is_restricted':('is_restricted',False,False,util.bool_converter)
}
labels = util.fill_in_column_definitions(properties,labels)
assert typecheck.isstring(path)
with open(path) as fh:
data = fh.read().decode(DEFAULT_ENCODING)
records = s2p.parse_sdf(data)
logger.info('rows read: %d ', len(records))
count = 0
for record in records:
initializer = {}
for key,properties in labels.items():
required = properties['required']
default = properties['default']
converter = properties['converter']
model_field = properties['model_field']
value = record.get(key)
try:
if(converter != None):
value = converter(value)
if(value == None ):
if( default != None ):
value = default
if(value == 'n/a'): value = None
if(value == None and required == True):
raise Exception(
'Field is required: %r, values: %r, row: %d'
% (key,initializer,count))
initializer[model_field] = value
except Exception, e:
logger.exception('invalid input, row: %d', count)
raise e
# follows is a kludge, to split up the entered "chemical_name" field,
# on ';' - TODO: just have two fields that get entered
if(initializer['name']):
initializer['alternative_names']=get_alternate_names(initializer['name'])
initializer['name']=get_primary_name(initializer['name'])
try:
sm = SmallMolecule(**initializer)
sm.save()
count += 1
# create a default batch - 0
SmallMoleculeBatch.objects.create(reagent=sm,batch_id=0)
except Exception:
logger.exception('save failed for: %r, row: %d', initializer, count)
raise