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 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'
if not attempts < 8:
raise Exception("Mysql", "Unable to get workunit with name: %s" % wuname)
#create instructions
for extein in exteinlist:
for nr in range(1,4):
if nr == 3:
if not shortpath:
for slicing in range(500):
uniqueforwu = pdbname + "_" + subunit + "_" + "linker" +"_" + extein + "_" + str(nr) + "_" + str(slicing) +"_"+ str(slicing + 1)
f = open(folder +"instructions" + "_" + uniqueforwu + ".csv", "w")
f.write(subunit +"," + uniqueforwu + "," + str(nr) + "," + str(slicing) +","+ str(slicing + 1) + "," + extein + "," "0")
f.close()
subprocess.call(["bin/stage_file", "--gzip", folder + "instructions" + "_" + uniqueforwu + ".csv"])
database.close()
subprocess.call(["bin/create_work", "--appname", "linker_generator", "--wu_template",
"templates/linker_gen.input-template", "--result_template", "templates/linker_gen.result-template", "--batch", str(jobid),
"--wu_name", uniqueforwu , "instructions" + "_" + uniqueforwu + ".csv", pdbfname])
database.connect()
setWuByName(uniqueforwu, igemdb.INIT)
else:
uniqueforwu = pdbname + "_" + subunit + "_" + "linker" +"_" + extein + "_" + str(nr) + "_" + "shortpath"
f = open(folder +"instructions" + "_" + uniqueforwu + ".csv", "w")
f.write(subunit +"," + uniqueforwu + "," + str(nr) + ",0,300" + "," + extein + "," + "1")
f.close()
subprocess.call(["bin/stage_file", "--gzip", folder + "instructions" + "_" + uniqueforwu + ".csv"])
database.close()
subprocess.call(["bin/create_work", "--appname", "linker_generator", "--wu_template",
"templates/linker_gen.input-template", "--result_template", "templates/linker_gen.result-template", "--batch", str(jobid),
