def run(self):
"""
This function runs the class in a loop unless the
one_pass or one_pass_WU_N flags are set. Before execution
parse_args() is called, the xml config file is loaded and
the SIGINT signal is hooked to the sigint_handler method.
"""
self.parse_args(sys.argv[1:])
self.config = configxml.default_config().config
# retrieve app where name = app.name
database.connect()
app=database.Apps.find1(name=self.appname)
database.close()
signal.signal(signal.SIGINT, self.sigint_handler)
# do one pass or execute main loop
if self.one_pass:
self.do_pass(app)
else:
# main loop
while(1):
database.connect()
workdone = self.do_pass(app)
database.close()
if not workdone:
time.sleep(self.sleep_interval)
def run(self):
"""
This function runs the class in a loop unless the
one_pass or one_pass_WU_N flags are set. Before execution
parse_args() is called, the xml config file is loaded and
the SIGINT signal is hooked to the sigint_handler method.
"""
self.parse_args(sys.argv[1:])
self.config = configxml.default_config().config
# retrieve app where name = app.name
database.connect()
app = database.Apps.find1(name=self.appname)
database.close()
signal.signal(signal.SIGINT, self.sigint_handler)
# do one pass or execute main loop
if self.one_pass:
self.do_pass(app)
else:
# main loop
while 1:
database.connect()
workdone = self.do_pass(app)
database.close()
if not workdone:
time.sleep(self.sleep_interval)
def user_details(userid):
"""
Fill user details from BOINC database
"""
user_line = UserInfo()
user_line.id = userid
database.connect()
user = database.Users.find(id=userid)[0]
user_line.name = user.name
user_line.email = user.email_addr
database.close()
return user_line
def user_details(userid):
"""
Fill user details from BOINC database
"""
user_line = UserInfo()
user_line.id = userid
database.connect()
user = database.Users.find(id=userid)[0]
user_line.name = user.name
user_line.email = user.email_addr
database.close()
return user_line
def run(self):
self.parse_args(sys.argv[1:])
self.config = configxml.default_config().config
# retrieve app where name = app.name
database.connect()
database.Apps.find1(name=self.appname)
conn = db_base.get_dbconnection()
user_count = 0
credit_count = 0
transaction = self._connection.begin()
query_cursor = conn.cursor()
delete_cursor = conn.cursor()
query_cursor.execute('select userid, workunitid from credited_job ')
results = query_cursor.fetchall()
for result in results:
user_count += 1
user_id = result['userid']
area_id = result['workunitid']
area_user = self._connection.execute(
select([AREA_USER]).where(
and_(AREA_USER.c.userid == user_id,
AREA_USER.c.area_id == area_id))).first()
if area_user is None:
area = self._connection.execute(
select([AREA]).where(AREA.c.area_id == area_id)).first()
galaxy_id = area['galaxy_id']
if area is None:
print 'Area', area_id, 'not found, User', user_id, 'not Credited'
else:
AREA_USER.insert().values(userid=user_id, area_id=area_id)
GALAXY_USER.insert().prefix_with('IGNORE').values(
userid=user_id, galaxy_id=galaxy_id)
print 'User', user_id, 'Credited for Area', area_id
credit_count += 1
delete_cursor.execute("delete from credited_job where userid = " +
str(user_id) + " and workunitid = " +
str(area_id))
transaction.commit()
conn.commit()
database.close()
self._connection.close()
print user_count, 'Users', credit_count, 'Credited'
def __init__(self, func, args=[], delay=RESULT_METER_DELAY):
'''Forks to print a progress meter'''
self.pid = os.fork()
if self.pid:
atexit.register(self.stop)
return
# re-open database
from Boinc import db_base, database
db_base.dbconnection = None
database.connect()
prev_s = None
while True:
s = func(*args)
if s != prev_s:
verbose_echo(1, s)
prev_s = s
time.sleep(delay)
def __init__(self, func, args=[], delay=RESULT_METER_DELAY):
'''Forks to print a progress meter'''
self.pid = os.fork()
if self.pid:
atexit.register(self.stop)
return
# re-open database
from Boinc import db_base, database
db_base.dbconnection = None
database.connect()
prev_s = None
while True:
s = apply(func, args)
if s != prev_s:
verbose_echo(1, s)
prev_s = s
time.sleep(delay)
def run(self):
self.parse_args(sys.argv[1:])
self.config = configxml.default_config().config
# retrieve app where name = app.name
database.connect()
database.Apps.find1(name=self.appname)
conn = db_base.get_dbconnection()
user_count = 0
credit_count = 0
transaction = self._connection.begin()
query_cursor = conn.cursor()
delete_cursor = conn.cursor()
query_cursor.execute('select userid, workunitid from credited_job ')
results = query_cursor.fetchall()
for result in results:
user_count += 1
user_id = result['userid']
area_id = result['workunitid']
area_user = self._connection.execute(select([AREA_USER]).where(and_(AREA_USER.c.userid == user_id, AREA_USER.c.area_id == area_id))).first()
if area_user is None:
area = self._connection.execute(select([AREA]).where(AREA.c.area_id == area_id)).first()
galaxy_id = area['galaxy_id']
if area is None:
print 'Area', area_id, 'not found, User', user_id, 'not Credited'
else:
AREA_USER.insert().values(userid=user_id, area_id=area_id)
GALAXY_USER.insert().prefix_with('IGNORE').values(userid=user_id, galaxy_id=galaxy_id)
print 'User', user_id, 'Credited for Area', area_id
credit_count += 1
delete_cursor.execute("delete from credited_job where userid = " + str(user_id) + " and workunitid = " + str(area_id))
transaction.commit()
conn.commit()
database.close()
self._connection.close()
print user_count, 'Users', credit_count, 'Credited'
# Merken: # # In Linkers.txt müssen die ganzen Linker sein, mit allen ausgetauschten Anfangs und Endsequenzen und auch den verschiedenen Winkelmotiven. exteinlist = ["RGKCWE", "CG"] startlist = ["GG", ""] databasefolder = "./import_files/" database.connect() #igemdb.connect() ####Hier kann man einfach hinter glob.glob() ein [:10] setzen, um das erstmal auf wengier laufen zu lassen und zu testen for folder in glob.glob(databasefolder + "*/")[:1]: pdbname = folder[-7:-3] pdbfname = pdbname + ".pdb" subunit = folder[-2] print "folder: %s, pdbname: %s, pdbfname: %s, subunit: %s" % (folder, pdbname, pdbfname, subunit) shortpath = return_shortpath(folder + pdbfname, subunit) #stage the PDB
def checkBatchComplete(self, wu): batchid = wu.batch database.connect() wus = database.Workunits.count(batch=batchid) finished_wus = database.Workunits.count(batch=batchid, assimilate_state=ASSIMILATE_DONE ) print "There are still %i unassimilated Workunits for Batch %i" % (wus-finished_wus, batchid)
