def connect(self, dbpath=None, configpath=None): #pylint: disable=too-many-branches, too-many-statements
"""Open a connection to the jobs database.
dbpath: path to a JobDB database file.
configpath: path to a pbs config file.
If dbpath is not given:
If PBS_JOB_DB environment variable exists, set dbpath to "$PBS_JOB_DB/jobs.db" file.
Else, set dbpath to "$HOME/.pbs/jobs.db", where $HOME is the user's home directory
If configpath is not given:
If PBS_JOB_DB environment variable exists, set configpath to
"$PBS_JOB_DB/config.json" file.
Else, set configpath to "$HOME/.pbs/config.json", where $HOME is
the user's home directory
"""
if dbpath is None:
if "PBS_JOB_DB" in os.environ:
dbpath = os.environ("PBS_JOB_DB")
if not os.path.isdir(dbpath):
print "Error in pbs.jobdb.JobDB.connect()."
print " PBS_JOB_DB:", dbpath
print " Does not exist"
sys.exit()
else:
dbpath = os.path.join(os.environ["HOME"], ".pbs")
if not os.path.isdir(dbpath):
print "Creating directory:", dbpath
os.mkdir(dbpath)
dbpath = os.path.join(dbpath, "jobs.db")
else:
if not os.path.isfile(dbpath):
print ("Error in pbs.jobdb.JobDB.connect(). argument dbpath =",
dbpath, "is not a file.")
sys.exit()
if configpath is None:
if "PBS_JOB_DB" in os.environ:
configpath = os.environ("PBS_JOB_DB")
if not os.path.isdir(configpath):
print "Error in pbs.jobdb.JobDB.connect()."
print " PBS_JOB_DB:", configpath
print " Does not exist"
sys.exit()
else:
configpath = os.path.join(os.environ["HOME"], ".pbs")
if not os.path.isdir(configpath):
print "Creating directory:", configpath
os.mkdir(configpath)
configpath = os.path.join(configpath, "config.json")
else:
if not os.path.isfile(configpath):
print ("Error in pbs.jobdb.JobDB.connect(). argument configpath =",
configpath, "is not a file.")
sys.exit()
if not os.path.isfile(configpath):
print "Writing Config:", configpath
self.config = {"software" : misc.getsoftware(), "version" : misc.getversion()}
with open(configpath, "w") as my_json:
json.dump(self.config, my_json, indent=0)
else:
with open(configpath) as my_json:
self.config = json.load(my_json)
if not os.path.isfile(dbpath):
print "Creating Database:", dbpath
self.conn = sqlite3.connect(dbpath)
self.conn.row_factory = sqlite3.Row
self.conn.create_function("REGEXP", 2, regexp)
self.curs = self.conn.cursor()
self.curs.execute("CREATE TABLE jobs " + sql_create_str())
self.conn.commit()
else:
self.conn = sqlite3.connect(dbpath)
self.conn.row_factory = sqlite3.Row
self.conn.create_function("REGEXP", 2, regexp)
self.curs = self.conn.cursor()
def _qstat(jobid=None, username=getlogin(), full=False, version=getversion()):
"""Return the stdout of qstat minus the header lines.
By default, 'username' is set to the current user.
'full' is the '-f' option
'id' is a string or list of strings of job ids
Returns the text of qstat, minus the header lines
"""
# -u and -f contradict in earlier versions of Torque
if full and username is not None and int(
version.split('.')[0]) < 5 and jobid is None:
# First get all jobs by the user
qopt = ["qselect"]
qopt += ["-u", username]
# Call 'qselect' using subprocess
q = subprocess.Popen(qopt,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT) #pylint: disable=invalid-name
stdout, stderr = q.communicate() #pylint: disable=unused-variable
qsout = StringIO.StringIO(stdout)
# Get the jobids
jobid = []
for line in qsout:
jobid += [line.rstrip("\n")]
opt = ["qstat"]
# If there are jobid(s), you don't need a username
if username is not None and jobid is None:
opt += ["-u", username]
# But if there are jobid(s) and a username, you need -a to get full output
elif username is not None and jobid is not None and not full:
opt += ["-a"]
# By this point we're guaranteed torque ver >= 5.0, so -u and -f are safe together
if full:
opt += ["-f"]
if jobid is not None:
if isinstance(jobid, str) or isinstance(jobid, unicode):
jobid = [jobid]
elif isinstance(jobid, list):
pass
else:
print "Error in pbs.misc.qstat(). type(jobid):", type(jobid)
sys.exit()
opt += jobid
# call 'qstat' using subprocess
# print opt
p = subprocess.Popen(opt, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) #pylint: disable=invalid-name
stdout, stderr = p.communicate() #pylint: disable=unused-variable
sout = StringIO.StringIO(stdout)
# strip the header lines
if full is False:
for line in sout:
if line[0] == "-":
break
# return the remaining text
return sout.read()