def get_profile(sqshrc="~/.sqshrc", connector="Sybase", hostname=None, username=None, password=None):
"""
get database, username, password from .sqshrc file e.g.
\set username="******"
"""
if connector == "Sybase":
shost, suser, spass = None, None, None
_ = lambda x: x.split("=")[-1].translate(None, "\"'").strip()
sqshrc = op.expanduser(sqshrc)
for row in open(sqshrc):
row = row.strip()
if not row.startswith("\\set") or "prompt" in row:
continue
if "password" in row:
spass = _(row)
if "hostname" in row:
shost = _(row)
if "username" in row:
suser = _(row)
if suser and spass:
username, password = suser, spass
if shost:
hostname = shost
dhost, duser, dpass = db_defaults(connector=connector)
if not password:
username, password = duser, dpass
elif not username:
username = getusername()
if not hostname:
hostname = dhost
return hostname, username, password
def kill(args):
"""
%prog kill [options] JOBNAMEPAT/JOBIDs
Kill jobs based on JOBNAME pattern matching (case-sensitive)
or list of JOBIDs (comma separated)
Examples:
%prog kill "pyth*" # Use regex
%prog kill 160253,160245,160252 # Use list of job ids
%prog kill all # Everything
"""
import shlex
from jcvi.apps.base import sh, getusername
from subprocess import check_output, CalledProcessError
import xml.etree.ElementTree as ET
valid_methods = ("pattern", "jobid")
p = OptionParser(kill.__doc__)
p.add_option(
"--method",
choices=valid_methods,
help="Identify jobs based on [default: guess]",
)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
username = getusername()
(tag, ) = args
tag = tag.strip()
if tag == "all":
sh("qdel -u {0}".format(username))
return
valid_jobids = set()
method = opts.method or guess_method(tag)
if method == "jobid":
jobids = tag.split(",")
valid_jobids |= set(jobids)
elif method == "pattern":
qsxmlcmd = 'qstat -u "{}" -j "{}" -nenv -njd -xml'.format(
username, tag)
try:
qsxml = check_output(shlex.split(qsxmlcmd)).strip()
except CalledProcessError as e:
qsxml = None
logging.debug(f'No jobs matching the pattern "{tag}": {e}')
if qsxml is not None:
for job in ET.fromstring(qsxml).findall("djob_info"):
for elem in job.findall("element"):
jobid = elem.find("JB_job_number").text
valid_jobids.add(jobid)
if valid_jobids:
sh("qdel {0}".format(",".join(valid_jobids)))
def kill(args):
"""
%prog kill [options] JOBNAMEPAT/JOBIDs
Kill jobs based on JOBNAME pattern matching (case-sensitive)
or list of JOBIDs (comma separated)
Examples:
%prog kill "pyth*" # Use regex
%prog kill 160253,160245,160252 # Use list of job ids
%prog kill all # Everything
"""
import shlex
from jcvi.apps.base import sh, getusername
from subprocess import check_output, CalledProcessError
import xml.etree.ElementTree as ET
valid_methods = ("pattern", "jobid")
p = OptionParser(kill.__doc__)
p.add_option("--method", choices=valid_methods,
help="Identify jobs based on [default: guess]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
username = getusername()
tag, = args
tag = tag.strip()
if tag == "all":
sh("qdel -u {0}".format(username))
return
valid_jobids = set()
method = opts.method or guess_method(tag)
if method == "jobid":
jobids = tag.split(",")
valid_jobids |= set(jobids)
elif method == "pattern":
qsxmlcmd = 'qstat -u "{0}" -j "{1}" -nenv -njd -xml'.\
format(username, tag)
try:
qsxml = check_output(shlex.split(qsxmlcmd)).strip()
except CalledProcessError as e:
qsxml = None
logging.debug('No jobs matching the pattern "{0}"'.format(tag))
if qsxml is not None:
for job in ET.fromstring(qsxml).findall("djob_info"):
for elem in job.findall("element"):
jobid = elem.find("JB_job_number").text
valid_jobids.add(jobid)
if valid_jobids:
sh("qdel {0}".format(",".join(valid_jobids)))
def get_profile(sqshrc="~/.sqshrc"):
"""
get database, username, password from .sqshrc file e.g.
\set username="******"
"""
_ = lambda x: x.split("=")[-1].translate(None, "\"'").strip()
sqshrc = op.expanduser(sqshrc)
for row in open(sqshrc):
row = row.strip()
if not row.startswith("\set"):
continue
if "password" in row:
password = _(row)
hostname = gethostname()
username = getusername()
return hostname, username, password
def get_profile(sqshrc="~/.sqshrc"):
"""
get database, username, password from .sqshrc file e.g.
\set username="******"
"""
_ = lambda x: x.split("=")[-1].translate(None, "\"'").strip()
sqshrc = op.expanduser(sqshrc)
for row in open(sqshrc):
row = row.strip()
if not row.startswith("\set"):
continue
if "password" in row:
password = _(row)
hostname = gethostname()
username = getusername()
return hostname, username, password
def get_profile(sqshrc="~/.sqshrc",
connector='Sybase',
hostname=None,
username=None,
password=None):
"""
get database, username, password from .sqshrc file e.g.
\set username="******"
"""
if connector == 'Sybase':
shost, suser, spass = None, None, None
_ = lambda x: x.split("=")[-1].translate(None, "\"'").strip()
sqshrc = op.expanduser(sqshrc)
if op.exists(sqshrc):
for row in open(sqshrc):
row = row.strip()
if not row.startswith("\\set") or "prompt" in row:
continue
if "password" in row:
spass = _(row)
if "hostname" in row:
shost = _(row)
if "username" in row:
suser = _(row)
else:
print >> sys.stderr, \
"[warning] file `{0}` not found".format(sqshrc)
if suser and spass:
username, password = suser, spass
if shost:
hostname = shost
dhost, duser, dpass = db_defaults(connector=connector)
if not password:
username, password = duser, dpass
elif not username:
username = getusername()
if not hostname:
hostname = dhost
return hostname, username, password