def insert_into_db(self, **args):
# create instance of database
db = RemoteDB()
# add process to db
db.add_updated_process(args['r'], args['s'], args['p'], args['m'], args['ma'], self.current_o_pro_pk)
# Indicate that the process was inserted successfully.
print "good update"
def insert_into_db(self, **args):
# create instance of database
db = RemoteDB()
# add process to db
db.add_updated_process(args['r'], args['s'], args['p'], args['m'],
args['ma'], self.current_o_pro_pk)
# Indicate that the process was inserted successfully.
print "good update"
def populate_kdb(self):
conn = self.connect_db(db=backup_db_name)
conn.execute(
'''SELECT pro_id, reactant_id, saddle_id, product_id FROM Process'''
)
process_list = conn.fetchall()
conn.close()
db = RemoteDB()
params = db.get_params()
if len(process_list) == 0:
print "No items in database to update."
return
print "Updating", db_name, "database."
for process in process_list:
reactant = db.get_atoms(process[1], db=backup_db_name)
saddle = db.get_atoms(process[2], db=backup_db_name)
product = db.get_atoms(process[3], db=backup_db_name)
mode = db.get_mode(process[1], db=backup_db_name)
self.current_o_pro_pk = process[0]
self.insert(reactant,
saddle,
product,
mode=mode,
nf=params['nf'],
dc=params['dc'],
mac=params['mac'])
def populate_kdb(self):
conn = self.connect_db(db=backup_db_name)
conn.execute('''SELECT pro_id, reactant_id, saddle_id, product_id FROM Process''')
process_list = conn.fetchall()
conn.close()
db = RemoteDB()
params = db.get_params()
if len(process_list) == 0:
print "No items in database to update."
return
print "Updating", db_name, "database."
for process in process_list:
reactant = db.get_atoms(process[1], db=backup_db_name)
saddle = db.get_atoms(process[2], db=backup_db_name)
product = db.get_atoms(process[3], db=backup_db_name)
mode = db.get_mode(process[1], db=backup_db_name)
self.current_o_pro_pk = process[0]
self.insert(reactant, saddle, product, mode=mode, nf=params['nf'], dc=params['dc'], mac=params['mac'])
def insert_into_db(self, **args):
#create database instance
db = RemoteDB()
# test if process is already in database
name = db.get_name(args['s'].get_chemical_symbols())
saddle_list = db.get_saddles(name)
for db_saddle in saddle_list:
if len(args['s']) != len(db_saddle[0]):
continue
if self.getMappings(args['s'], db_saddle[0], args['nf'],
args['dc']) is not None:
#print "SQL duplicate of", name, "with id:", db_saddle[1]
return "SQL duplicate of " + name + " with id: " + str(
db_saddle[1])
# add process to db
try:
db.add_process(args['or'], args['os'], args['op'], args['om'],
args['r'], args['s'], args['p'], args['m'],
args['ma'], self.email, self.password)
except TypeError:
print "Account info in user_config.py is not valid. Try running remote_config.py to set up account"
return
# Indicate that the process was inserted successfully.
#print "good"
return "good"
def insert_into_db(self, **args):
#create database instance
db = RemoteDB()
# test if process is already in database
name = db.get_name(args['s'].get_chemical_symbols())
saddle_list = db.get_saddles(name)
for db_saddle in saddle_list:
if len(args['s']) != len(db_saddle[0]):
continue
if self.getMappings(args['s'], db_saddle[0], args['nf'], args['dc']) is not None:
print "SQL duplicate of", name, "with id:", db_saddle[1]
return "SQL duplicate of " + name + " with id: " + str(db_saddle[1])
# add process to db
try:
db.add_process(args['or'], args['os'], args['op'], args['om'],
args['r'], args['s'], args['p'], args['m'], args['ma'], self.email, self.password)
except TypeError:
print "Account info in user_config.py is not valid. Try running remote_config.py to set up account"
return
# Indicate that the process was inserted successfully.
print "good"
return "good"
def query_db(self, **args):
db = RemoteDB()
name = db.get_name(args['reactant'].get_chemical_symbols())
entries = db.get_process(name)
return entries, name
# overloads KdbQuery.query_db()
def query_db(self, **args):
db = RemoteDB()
name = db.get_name(args['reactant'].get_chemical_symbols())
entries = db.get_process(name)
return entries, name
def output_query(self, outpurdir, numMatches, suggestion, sugproduct, modeTemp=None):
self.return_dict[numMatches] = [suggestion, sugproduct]
if modeTemp is not None:
self.return_dict[numMatches].append(modeTemp)
if __name__ == "__main__":
# Parse command line options.
parser = OptionParser(usage = "%prog [options] reactant.con")
parser.add_option("--nodupes", dest = "nodupes", action="store_true",
help = "detect and remove duplicate suggestions (can be expensive)")
options, args = parser.parse_args()
# Make sure we get the reactant file name.
if len(args) < 1:
parser.print_help()
sys.exit()
# Load the reactant con file.
reactant = read_any(args[0])
db = RemoteDB()
params = db.get_params()
query_sub_class = RemoteQuery()
query_sub_class.query(reactant, "./kdbmatches_remote", dc=params['dc'], nf=params['nf'], nodupes=options.nodupes, kdbname=db_name)
default=None)
options, args = parser.parse_args()
# Make sure we get the reactant, saddle, product, and mode files.
if len(args) < 3:
parser.print_help()
sys.exit()
# Load the reactant, saddle, product, and mode files.
reactant = read_any(args[0])
saddle = read_any(args[1])
product = read_any(args[2])
mode = None
if options.mode is not None:
mode = insert_sub_class.load_mode(options.mode)
# load previous params
db = RemoteDB()
params = db.get_params()
nf = params['nf']
dc = params['dc']
mac = params['mac']
insert_sub_class.insert(reactant,
saddle,
product,
mode,
nf=nf,
dc=dc,
mac=mac)
def query_db(self, **args):
db = RemoteDB()
name = db.get_name(args['reactant'].get_chemical_symbols())
entries = db.get_process(name)
return entries, name