def insert_fred_scores(r_id, c_id, p_id, chargeset, tautomers, scores):
if scores != None and len(scores) != 0:
vals = '({0})'.format(', '.join(map(str, [r_id,c_id, p_id, chargeset, tautomers] + scores)))
stm = "insert into BindingScoresFred values\n{0}".format(vals)
else:
stm = "insert into BindingScoresFred (receptor_id, compound_id, pose_id, chargeset_id, tautomers) " +\
"values ({0},{1},{2},{3},{4})".format(r_id,c_id, p_id, chargeset, tautomers)
conn = mddb_utils.get_dbconn(dbname, dbuser, dbhost, dbpass)
mddb_utils.execute_query(conn, stm)
def insert_dock6_amber_scores(r_id, c_id, p_id, chargeset, tautomers, list_of_score_tups):
if list_of_score_tups != None and len(list_of_score_tups) != 0:
vals = ',\n'.join(
map(lambda x: '({0})'.format(', '.join(map(str, [r_id,c_id, p_id, chargeset, tautomers] + list(x)))), list_of_score_tups)
)
stm = "insert into BindingScoresDock6Amber values\n{0}".format(vals)
else:
stm = "insert into BindingScoresDock6Amber (receptor_id, compound_id, pose_id, chargeset_id, tautomers) " +\
"values ({0},{1},{2},{3},{4})".format(r_id,c_id, p_id, chargeset, tautomers)
conn = mddb_utils.get_dbconn(dbname, dbuser, dbhost, dbpass)
mddb_utils.execute_query(conn, stm)
def load_configs(self):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
c_id_all = mddb_utils.execute_query(conn, "select insert_new_config('charmm', 'all')")
self.load_config(c_id_all, '/damsl/mddb/data/amino_configs/config_charmm')
c_id_ua = mddb_utils.execute_query(conn, "select insert_new_config('charmm', 'ua')")
self.load_config(c_id_ua, '/damsl/mddb/data/amino_configs/config_ua_charmm')
#mddb_utils.load_machine_info(conn, ['mddb','mddb2','qp2','qp3','qp4','qp5','qp6'])
conn.commit()
conn.close()
def sample_loop(self):
while True:
#try:
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
res = mddb_utils.execute_query(conn,
"select param_value from ControlParams where param_name = 'sampleloop'")
print datetime.datetime.now()
try:
nt = mddb_utils.execute_query(conn, "select resample_blocking(E'{gmdhost}:{gmdport}')".format(**self.param_dict))
except Exception as e:
m = "Error {0}".format(str(e))
print m
try:
mddb_utils.execute_query(conn, "insert into ErrorMessages values (statement_timestamp(),{0},{1})".format("sample_loop", m.encode("utf-8")))
except:
pass
nt = 0
time.sleep(2)
continue
if int(nt) > 0:
time.sleep(0.05)
else:
time.sleep(2)
print res
if res == 'quitting':
mddb_utils.execute_query(conn,
"select controlparams_upsert('sampleloop', 'notrunning')")
mddb_utils.execute_query(conn,
"update ExpJobs set active = False;")
conn.close()
break
cur = conn.cursor()
cur.execute('select S.subspace_id from subspaces S, expjobs E where S.subspace_id = E.subspace_id group by S.subspace_id having bool_or(active)')
num_active_subspaces = cur.rowcount
if num_active_subspaces == 0:
cur = conn.cursor(cursor_factory=psycopg2.extras.RealDictCursor)
cur.execute('select * from mdq_pop()')
if cur.rowcount > 0:
ss_dict = cur.fetchone()
if any(ss_dict.values()):
ss_dict['protein_seq'] = "".join(ss_dict['expanded_terms'])
mddb_utils.subspace_init(dict(self.param_dict.items() + ss_dict.items()))
cur.close()
conn.commit()
conn.close()
def start_sampleloop(self):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
prefix = os.path.join(os.getenv('HOME'),
self.param_dict['user'],
controller.Controller.mwd)
pp = controller.Controller.centos_pythonpaths.format(prefix)
env = "PYTHONPATH={0} GPHOME=/opt/greenplum-db/. PGHOST=localhost4 PGOPTIONS=--client-min-messages=error ".format(pp)
env = env + "PATH={PATH} LD_LIBRARY_PATH={LD_LIBRARY_PATH} ".format(**os.environ)
self.param_dict['env'] = env
sample_loop_cmd = ("""screen -S {dbname}_{user}_sample_loop -d -m """+\
"""env {env}""" +\
"""/opt/greenplum-db/ext/python/bin/python """+ os.path.abspath( __file__ ) +\
""" --mode loop """+\
""" --dbname {dbname} """+\
""" --dbpass {dbpass} """+\
""" 2>&1 | tee /tmp/{dbname}_{user}_sampleloop.log >&1 """).format(**self.param_dict);
mddb_utils.run_cmd(sample_loop_cmd)
mddb_utils.execute_query(conn,
"select controlparams_upsert('sampleloop', 'running')")
conn.commit()
conn.close()
def setup_workers(self, l):
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
for d in l:
h = d['hostname']
self.param_dict['res_config_name'] = d.get('res_config_name') or 'default'
self.param_dict['avg_seq_jobs'] = d.get('avg_seq_jobs') or 1
self.prepare_worker(h)
prefix = os.path.join(os.getenv('HOME'),
self.param_dict['user'],
self.param_dict['mwd'])
self.param_dict['remotegen'] = ""
self.param_dict['gen_host'] = h
remote_resource_names = [k for k,v in resources.resource_dict.items() if v != resources.LocalResource]
if h in remote_resource_names:
self.param_dict['worker_host'] = 'localhost'
else:
self.param_dict['worker_host'] = self.param_dict['gen_host']
# centos hosts reqires a different PYTHONPATH than ubuntu hosts
# TODO: add more centos hosts all qp-hm* and qp-hd*
if self.param_dict['worker_host'] in ['mddb', 'mddb2', 'localhost']:
self.param_dict['pythonpaths'] = self.centos_pythonpaths.format(prefix)
else:
self.param_dict['pythonpaths'] = self.ubuntu_pythonpaths.format(prefix)
# insert the worker name into the 'workers' table
i = mddb_utils.execute_query(conn, "select workers_insert('{gen_host}');".format(**self.param_dict))
self.param_dict['worker_id'] = i
self.param_dict['worker_name'] = "gmw_{dbname}_{gen_host}_{worker_id}_{user}".format(**self.param_dict)
self.start_gmw(conn)
conn.commit()
conn.close()
def result_exists(conn, tn, r_id, c_id, p_id, chargeset, tautomers):
stm = "select 1 from {0} where receptor_id = {1} and compound_id = {2} and pose_id = {3} and chargeset_id = {4} and tautomers = {5}".format(tn, r_id, c_id, p_id, chargeset, tautomers)
return mddb_utils.execute_query(conn, stm) != None
