def filldatabase(fingerprintdf):
mysession = SQLSession(Schemas.qsar_schema).get_session()
username = '******'
descriptors_index = 1448
compound_descriptor_set_objects = []
# print(fingerprintdf)
for index, row in fingerprintdf.iterrows():
efk_dsstox_compound_id = row[0].split('0', 1)[1]
fk_descriptor_set_id = descriptors_index
xx = [str(x) for x in list(row[1])]
descriptor_string_tsv = '\t'.join(xx)
created_by = username
updated_by = username
compound_descriptor_sets = CompoundDescriptorSets(
efk_dsstox_compound_id=efk_dsstox_compound_id,
descriptor_string_tsv=descriptor_string_tsv,
created_by=created_by,
fk_descriptor_set_id=fk_descriptor_set_id,
updated_by=updated_by)
compound_descriptor_set_objects.append(compound_descriptor_sets)
mysession.bulk_save_objects(compound_descriptor_set_objects)
mysession.commit()
def filldatabase(yourlist, desc_set_id, prefix):
username = '******'
descriptors_index = desc_set_id
mysession = SQLSession(Schemas.qsar_schema).get_session()
descriptor_objects = []
for index, val in enumerate(yourlist):
fk_descriptor_set_id = descriptors_index
index_number = index + 1
# xx = [str(x) for x in list(row)]
descriptors_name = str(prefix.format(index + 1))
created_by = username
updated_by = username
long_description = ''
short_description = ''
label = val
descriptor = Descriptors(index_number=index_number,
descriptors_name=descriptors_name,
long_description=long_description,
short_description=short_description,
label=label,
created_by=created_by,
fk_descriptor_set_id=fk_descriptor_set_id,
updated_by=updated_by)
descriptor_objects.append(descriptor)
mysession.bulk_save_objects(descriptor_objects)
mysession.commit()
def updatedatabase(fingerprintdf):
username = '******'
descriptors_index = 1448
# Query for compound_descriptor_sets.id
mysession = SQLSession(Schemas.qsar_schema).get_session()
query3 = mysession.query(Compounds.dsstox_compound_id, CompoundDescriptorSets.id) \
.join(CompoundDescriptorSets, Compounds.id == CompoundDescriptorSets.efk_dsstox_compound_id).filter(CompoundDescriptorSets.fk_descriptor_set_id == descriptors_index)
df3 = pd.DataFrame(list(query3))
#join query with fingerprintdf
mytable = pd.merge(df3, fingerprintdf, on='dsstox_compound_id')
# # # CODE FOR UPDATING # # #
for index, row in mytable.iterrows():
id = row[1]
descriptor_string_tsv = row[2]
updated_by = username
mysession.query(CompoundDescriptorSets.id,
CompoundDescriptorSets.descriptor_string_tsv,
CompoundDescriptorSets.updated_by).filter(
CompoundDescriptorSets.id == id).update({
"descriptor_string_tsv":
descriptor_string_tsv,
"updated_by":
updated_by
})
mysession.commit()
def update_toxprint_database(fingerprintdf):
username = '******'
descriptors_index = 1445
# Query for compound_descriptor_sets.id
mysession = SQLSession(Schemas.qsar_schema).get_session()
query3 = mysession.query(CompoundDescriptorSets.id, CompoundDescriptorSets.efk_dsstox_compound_id)\
.filter(CompoundDescriptorSets.fk_descriptor_set_id == descriptors_index)
df3 = pd.DataFrame(list(query3))
#join query with fingerprintdf
fingerprintdf = fingerprintdf.reset_index()
fingerprintdf = fingerprintdf.rename(
columns={'M_NAME':
'efk_dsstox_compound_id'}) # not sure this will work
fingerprintdf['efk_dsstox_compound_id'] = [
int(x[8:]) for x in fingerprintdf['efk_dsstox_compound_id']
]
mytable = pd.merge(df3, fingerprintdf, on='efk_dsstox_compound_id')
# # # CODE FOR UPDATING # # #
for index, row in mytable.iterrows():
id = str(row[0])
xx = [str(x) for x in list(row[2:])]
descriptor_string_tsv = '\t'.join(xx)
updated_by = username
mysession.query(CompoundDescriptorSets.id,
CompoundDescriptorSets.descriptor_string_tsv,
CompoundDescriptorSets.updated_by).filter(
CompoundDescriptorSets.id == id).update({
"descriptor_string_tsv":
descriptor_string_tsv,
"updated_by":
updated_by
})
mysession.commit()
def filluc(invitrodbdf, mydatasetid):
#set starttime
starttime = time.time()
username = '******'
descriptor_set_id = [1445, 1447, 1446, 1448]
# descriptor_set_id = [1448] # <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
# 1445 = toxprints
# 1446 = MACCS
# 1447 = pubchem
# 1448 = Special Toxprints
for id in descriptor_set_id:
# add enrichment table to the mysql database
try:
filled_table = handle_duplicates(invitrodbdf.loc[:, ['dsstox_compound_id', 'hitc']])
except:
print("DUPLICATE HANDLER FAILED: {}".format(mydatasetid))
sys.exit(1)
try:
filled_table = fillfp(filled_table, id)
except:
print("FILLFP FAILED: {}".format(mydatasetid))
sys.exit(1)
# filled_table = pd.DataFrame(filled_table)
try:
my_enrichment_table = enrich(filled_table)
except:
print("ENRICH FAILED: {}".format(mydatasetid))
print(filled_table.head())
sys.exit(1)
# add fk_descriptor_id
### CHECK THAT THESE ARE MATCHING! ###
mysession2 = SQLSession(Schemas.qsar_schema).get_session()
query3 = mysession2.query(Descriptors.id).filter(Descriptors.fk_descriptor_set_id == id)
query3 = list(query3)
query3 = [int(i[0]) for i in query3]
my_enrichment_table.insert(0, 'fk_descriptor_id', query3)
for index, row in my_enrichment_table.iterrows():
fk_dataset_id = int(mydatasetid)
fk_descriptor_id = int(row['fk_descriptor_id'])
univariate_calc = UnivariateCalculations(fk_dataset_id=fk_dataset_id,
fk_descriptor_id=fk_descriptor_id,
updated_by=username,
created_by=username)
mysession2.add(univariate_calc)
mysession2.flush()
fk_univ_calc_id = int(univariate_calc.id)
### NEED TO CHANGE for loop & stat_list IF THE STATISTICS ARE CHANGED IN Enrichment_Table_Generator ###
count = 0
for i in row[1:]:
if math.isnan(i):
value = None
elif math.isinf(i):
value = 99999999.9
else:
value = float(i)
stat_list = [9, 10, 11, 12, 13, 4, 8, 7, 14, 15]
fk_statistic_id = int(stat_list[count])
uc_statistics = UcStatistics(value=value,
fk_univ_calc_id=int(fk_univ_calc_id),
fk_statistic_id=int(fk_statistic_id),
created_by=username,
updated_by=username)
mysession2.add(uc_statistics)
count += 1
mysession2.commit()
# mysession2.close()
endtime = time.time()
print('run time:{}'.format(endtime-starttime))
aeid_data[0] = [int(x) for x in aeid_data[0]]
aeid_data = aeid_data.sort_values(0, axis=0)
aeid_data = aeid_data.reset_index(drop=True)
# print(aeid_data)
# sys.exit(1)
# add ASSAY_COMPONENT_ENDPOINT_NAME as descriptors.label
# use aeid as descriptors_name
for i, row in aeid_data.iterrows():
username = '******'
# create a new datasets name entry
description = "Hit Calls from MC5 for the toxcast AEID: {} taken on the date:{}" \
.format(row[0], datetime.datetime.today().strftime("%Y%m%d"))
descriptors = Descriptors(fk_descriptor_set_id='1449',
index_number=str(i + 1),
descriptors_name='AEID-{}'.format(row[0]),
label=row[1],
updated_by=username,
created_by=username,
long_description=description,
short_description=description)
mysession.add(descriptors)
# mysession.flush()
# fk_dataset_id = int(datasets.id)
mysession.commit()
# sys.exit(1)
