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postgresql.py
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postgresql.py
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import psycopg2
class DB(object):
"""Helper class to Traj for database handling"""
def __init__(self,projname,casename,
host="localhost",database="trajs",user="postgres"):
""" Initialize connection to database """
self.conn = psycopg2.connect(database=database,host=host,
user=user)
self.c = self.conn.cursor()
self.tablename = ("%s%s" % (projname ,casename)).lower()
def drop_all_tables(self, tablename, really=False):
"""Drop master and inherited tables in a partition"""
if really:
sql = "SELECT tablename FROM pg_tables WHERE tablename LIKE '%s%%';"
self.c.execute(sql % tablename)
tablelist = self.c.fetchall()
for table in tablelist:
print table
self.c.execute("DROP TABLE %s;" % table)
self.conn.commit()
def table_exists(self, table_name):
""" Check if an index already exists in the DB """
sql = "SELECT tablename FROM pg_tables WHERE tablename LIKE '%s';"
self.c.execute(sql % table_name.lower())
if self.c.rowcount > 0:
return True
else:
return False
def create_table(self,tablename=None):
"""Create a postgres table for tracmass data"""
if not tablename: tablename = self.tablename
if self.table_exists(tablename): return
CT1 = "CREATE TABLE %s " % tablename
CT2 = "( runid INT, ints float8, ntrac INT, x REAL ,y REAL, z REAL )"
self.c.execute(CT1 + CT2)
self.conn.commit()
def create_partition(self,tablename,partition):
if self.table_exists(partition): return
self.create_table(tablename)
sql= "CREATE TABLE %s ( ) INHERITS (%s);"
self.c.execute(sql % (partition, tablename))
self.conn.commit()
def create_bulkload_table(self):
"""Create a temporary postgres table for bulkload of data """
if self.table_exists("temp_bulkload"): return
CT1 = "CREATE TABLE temp_bulkload "
CT2 = "( ntrac INT, ints float8, x REAL, y REAL, z REAL)"
self.c.execute(CT1 + CT2)
self.conn.commit()
def generate_runid(self, jd1=None, jd2=None, temp=False,
tablename=None,filename=''):
"""Find or generate row for current run in runs."""
if not tablename: tablename = self.tablename
def insert_runid(jd1,jd2):
sql = ("INSERT INTO runs (jd1,jd2,tablename,filename) " +
" values (%s,%s,%s,%s) RETURNING id" )
self.c.execute(sql, (jd1, jd2, tablename, filename) )
self.conn.commit()
return self.c.fetchone()[0]
if temp:
return insert_runid(-999, -998)
else:
if not jd1: jd1,jd2 = (self.jd.min(),self.jd.max())
sql = ("SELECT id FROM runs " +
" WHERE jd1=%s AND jd2=%s AND tablename='%s'" %
(jd1, jd2, tablename))
self.c.execute(sql )
id = self.c.fetchall()
if len(id) == 1:
return id[0][0]
elif len(id) == 0:
return insert_runid(jd1,jd2)
else:
raise ValueError,"More than one runid in database"
def index_exists(self, index_name):
""" Check if an index exists in the DB """
sql = "SELECT * FROM pg_indexes WHERE indexname LIKE '%s';"
self.c.execute(sql % index_name.lower())
if self.c.rowcount > 0:
return True
else:
return False
def add_primary_keys(self, tablename):
if not self.index_exists("%s_pkey" % tablename):
sql = "ALTER TABLE %s ADD PRIMARY KEY (runid,ints,ntrac);"
self.c.execute(sql % ("%s" % tablename) )
self.conn.commit()
def add_index(self, tablename, indexname, rows):
index = "%s_%s_idx" % (indexname, tablename)
if not self.index_exists(index):
sql = "CREATE INDEX %s ON %s USING btree (%s)"
self.c.execute(sql % (index, tablename, rows ))
self.conn.commit()
def create_indexes(self):
""" Create all missing indexes """
sql = "SELECT distinct(tablename) FROM runs;"
self.c.execute(sql)
rowlist = self.c.fetchall()
for row in rowlist:
t1 = dtm.now()
print row[0]
add_primary_keys(row[0])
print "Time passed: ",dtm.now()-t1
add_index(self, row[0], 'ints', 'ints')
print "Time passed: ",dtm.now()-t1
add_index(self, row[0], 'runtrac', 'runid,ntrac')
print "Time passed: ",dtm.now()-t1
batch.purge()
def remove_earlier_data_from_table(self, runid):
self.c.execute("SELECT DISTINCT(runid) FROM %s;" %self.tablename)
if self.c.rowcount > -2:
DL = ( "DELETE FROM %s WHERE runid=%s;" %
(self.tablename,runid) )
print "Any old posts with runid=%s deleted." % (runid)
else :
DL = "TRUNCATE TABLE %s;" % self.tablename
print "The table %s was truncated." % self.tablename
#self.create_indexes()
self.c.execute(DL)
self.conn.commit()
def insert(self, db="trm"):
"""Insert trajectories from Traj into database"""
self.create_table()
id = self.generate_runid()
print id
self.remove_earlier_data_from_table(id)
sql = ("INSERT INTO " + self.tablename +
" (runid, ntrac, ints, x, y, z) " +
" values (%s,%s,%s,%s,%s,%s)")
vals = izip((self.x*0+id).astype('float'),
self.ntrac.astype('float'),
self.ints.astype('float'), self.x.astype('float'),
self.y.astype('float'), self.z.astype('float'))
self.c.executemany(sql,vals)
def tablejds(self,jd):
return "%s_%i_%i" % (self.tablename, int(jd/10)*10, int(jd/10)*10+10)
def bulkinsert(self,datafile=None):
"""Insert trm bin-files data using pg_bulkload"""
pg_bulkload = "/opt/local/lib/postgresql90/bin/pg_bulkload"
ctl_file = "load_trm.ctl"
db = "-dpartsat"
outtable = "-O" + "temp_bulkload" # self.tablename
def run_command(datafile):
t1 = dtm.now()
sql = "truncate table temp_bulkload;"
self.c.execute(sql)
self.conn.commit()
infile = "-i%s/%s" % (self.datadir, datafile)
spr.call([pg_bulkload,ctl_file,db,infile,outtable])
print "Elapsed time: " + str(dtm.now()-t1)
sql = "SELECT min(ints),max(ints) FROM temp_bulkload;"
self.c.execute(sql)
jd1,jd2 = self.c.fetchall()[0]
tablename = self.tablejds(jd1)
runid = self.generate_runid(jd1=jd1, jd2=jd2,filename = datafile,
tablename=tablename)
print "Elapsed time: " + str(dtm.now()-t1)
self.create_partition(self.tablename, tablename)
sql1 = "INSERT INTO %s (runid,ints,ntrac,x,y,z) " % tablename
sql2 = " SELECT %i as runid,ints,ntrac,x,y,z " % runid
sql3 = " FROM temp_bulkload;"
self.c.execute(sql1 + sql2 + sql3)
self.conn.commit()
print "Elapsed time: " + str(dtm.now()-t1)
batch.purge()
if datafile:
run_command(datafile)
else:
flist = glob.glob( "%s/%s*_run.bin" % (self.datadir,
self.datafile))
for f in flist: run_command(os.path.basename(f))
def copy(self):
if len(self.x) == 0: return False
self.create_table()
id = self.generate_runid()
self.remove_earlier_data_from_table(id)
vf = cStringIO.StringIO()
mat = np.vstack( ((self.jd*0+1).astype(np.int),self.jd,self.ntrac,
self.x, self.y, self.z) ).T
np.savetxt(vf,mat,fmt=('%i %f %i %f %f %f') )
vf.seek(0)
self.c.copy_from(vf,self.tablename,sep=' ')
self.conn.commit()
def select(self,jd=None, runid=0, ints=0, ntrac=0):
""" Retrive trajectories from database """
if not jd: jd = ints
whstr = ""
if runid != 0: whstr += " runid = %i AND" % runid
if ints != 0: whstr += " ints = %i AND" % ints
if ntrac != 0: whstr += " ntrac = %i " % ntrac
whstr = whstr.rstrip("AND")
self.c.execute('SELECT * FROM %s WHERE %s' %
(self.tablename,whstr) )
return zip(*self.c.fetchall())