#!/usr/bin/env python
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
import logging
import argparse
import json
import tempfile
+import errno
parser = argparse.ArgumentParser()
parser.add_argument('--dry-run', action='store_true')
-parser.add_argument('--job-parameters', type=str, default="{}")
+parser.add_argument('--script-parameters', type=str, default="{}")
args = parser.parse_args()
os.umask(0077)
taskp = arvados.current_task()['parameters']
else:
outdir = "/tmp"
- jobp = json.loads(args.job_parameters)
+ jobp = json.loads(args.script_parameters)
os.environ['JOB_UUID'] = 'zzzzz-8i9sb-1234567890abcde'
os.environ['TASK_UUID'] = 'zzzzz-ot0gb-1234567890abcde'
- os.environ['CRUNCH_SRC'] = '/tmp/crunche-src'
+ os.environ['CRUNCH_SRC'] = '/tmp/crunch-src'
if 'TASK_KEEPMOUNT' not in os.environ:
os.environ['TASK_KEEPMOUNT'] = '/keep'
-links = []
-
def sub_tmpdir(v):
return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
def __init__(self):
self.sig = None
- def send_signal(self, sp, signum):
- sp.send_signal(signum)
+ def send_signal(self, subprocesses, signum):
+ for sp in subprocesses:
+ sp.send_signal(signum)
self.sig = signum
+# http://rightfootin.blogspot.com/2006/09/more-on-python-flatten.html
+def flatten(l, ltypes=(list, tuple)):
+ ltype = type(l)
+ l = list(l)
+ i = 0
+ while i < len(l):
+ while isinstance(l[i], ltypes):
+ if not l[i]:
+ l.pop(i)
+ i -= 1
+ break
+ else:
+ l[i:i + 1] = l[i]
+ i += 1
+ return ltype(l)
+
def add_to_group(gr, match):
- m = ('^_^').join(match.groups())
+ m = match.groups()
if m not in gr:
gr[m] = []
gr[m].append(match.group(0))
+class EvaluationError(Exception):
+ pass
+
+# Return the name of variable ('var') that will take on each value in 'items'
+# when performing an inner substitution
+def var_items(p, c, key):
+ if key not in c:
+ raise EvaluationError("'%s' was expected in 'p' but is missing" % key)
+
+ if "var" in c:
+ if not isinstance(c["var"], basestring):
+ raise EvaluationError("Value of 'var' must be a string")
+ # Var specifies the variable name for inner parameter substitution
+ return (c["var"], get_items(p, c[key]))
+ else:
+ # The component function ('key') value is a list, so return the list
+ # directly with no parameter selected.
+ if isinstance(c[key], list):
+ return (None, get_items(p, c[key]))
+ elif isinstance(c[key], basestring):
+ # check if c[key] is a string that looks like a parameter
+ m = re.match("^\$\((.*)\)$", c[key])
+ if m and m.group(1) in p:
+ return (m.group(1), get_items(p, c[key]))
+ else:
+ # backwards compatible, foreach specifies bare parameter name to use
+ return (c[key], get_items(p, p[c[key]]))
+ else:
+ raise EvaluationError("Value of '%s' must be a string or list" % key)
+
+# "p" is the parameter scope, "c" is the item to be expanded.
+# If "c" is a dict, apply function expansion.
+# If "c" is a list, recursively expand each item and return a new list.
+# If "c" is a string, apply parameter substitution
def expand_item(p, c):
if isinstance(c, dict):
if "foreach" in c and "command" in c:
- var = c["foreach"]
- items = get_items(p, p[var])
+ # Expand a command template for each item in the specified user
+ # parameter
+ var, items = var_items(p, c, "foreach")
+ if var is None:
+ raise EvaluationError("Must specify 'var' in foreach")
r = []
for i in items:
params = copy.copy(p)
params[var] = i
- r.extend(expand_list(params, c["command"]))
+ r.append(expand_item(params, c["command"]))
return r
- if "list" in c and "index" in c and "command" in c:
- var = c["list"]
- items = get_items(p, p[var])
+ elif "list" in c and "index" in c and "command" in c:
+ # extract a single item from a list
+ var, items = var_items(p, c, "list")
+ if var is None:
+ raise EvaluationError("Must specify 'var' in list")
params = copy.copy(p)
params[var] = items[int(c["index"])]
- return expand_list(params, c["command"])
- if "regex" in c:
+ return expand_item(params, c["command"])
+ elif "regex" in c:
pattern = re.compile(c["regex"])
if "filter" in c:
- items = get_items(p, p[c["filter"]])
+ # filter list so that it only includes items that match a
+ # regular expression
+ _, items = var_items(p, c, "filter")
return [i for i in items if pattern.match(i)]
elif "group" in c:
- items = get_items(p, p[c["group"]])
+ # generate a list of lists, where items are grouped on common
+ # subexpression match
+ _, items = var_items(p, c, "group")
groups = {}
for i in items:
- p = pattern.match(i)
- if p:
- add_to_group(groups, p)
+ match = pattern.match(i)
+ if match:
+ add_to_group(groups, match)
return [groups[k] for k in groups]
elif "extract" in c:
- items = get_items(p, p[c["extract"]])
+ # generate a list of lists, where items are split by
+ # subexpression match
+ _, items = var_items(p, c, "extract")
r = []
for i in items:
- p = pattern.match(i)
- if p:
- r.append(list(p.groups()))
+ match = pattern.match(i)
+ if match:
+ r.append(list(match.groups()))
return r
+ elif "batch" in c and "size" in c:
+ # generate a list of lists, where items are split into a batch size
+ _, items = var_items(p, c, "batch")
+ sz = int(c["size"])
+ r = []
+ for j in xrange(0, len(items), sz):
+ r.append(items[j:j+sz])
+ return r
+ raise EvaluationError("Missing valid list context function")
elif isinstance(c, list):
- return expand_list(p, c)
+ return [expand_item(p, arg) for arg in c]
elif isinstance(c, basestring):
- return [subst.do_substitution(p, c)]
-
- return []
-
-def expand_list(p, l):
- if isinstance(l, basestring):
- return expand_item(p, l)
+ m = re.match("^\$\((.*)\)$", c)
+ if m and m.group(1) in p:
+ return expand_item(p, p[m.group(1)])
+ else:
+ return subst.do_substitution(p, c)
else:
- return [exp for arg in l for exp in expand_item(p, arg)]
+ raise EvaluationError("expand_item() unexpected parameter type %s" % type(c))
+# Evaluate in a list context
+# "p" is the parameter scope, "value" will be evaluated
+# if "value" is a list after expansion, return that
+# if "value" is a path to a directory, return a list consisting of each entry in the directory
+# if "value" is a path to a file, return a list consisting of each line of the file
def get_items(p, value):
- if isinstance(value, dict):
- return expand_item(p, value)
-
+ value = expand_item(p, value)
if isinstance(value, list):
- return expand_list(p, value)
-
- fn = subst.do_substitution(p, value)
- mode = os.stat(fn).st_mode
- prefix = fn[len(os.environ['TASK_KEEPMOUNT'])+1:]
- if mode is not None:
- if stat.S_ISDIR(mode):
- items = [os.path.join(fn, l) for l in os.listdir(fn)]
- elif stat.S_ISREG(mode):
- with open(fn) as f:
- items = [line.rstrip("\r\n") for line in f]
- return items
- else:
- return None
+ return value
+ elif isinstance(value, basestring):
+ mode = os.stat(value).st_mode
+ prefix = value[len(os.environ['TASK_KEEPMOUNT'])+1:]
+ if mode is not None:
+ if stat.S_ISDIR(mode):
+ items = [os.path.join(value, l) for l in os.listdir(value)]
+ elif stat.S_ISREG(mode):
+ with open(value) as f:
+ items = [line.rstrip("\r\n") for line in f]
+ return items
+ raise EvaluationError("get_items did not yield a list")
stdoutname = None
stdoutfile = None
stdinname = None
stdinfile = None
-rcode = 1
+# Construct the cross product of all values of each variable listed in fvars
def recursive_foreach(params, fvars):
var = fvars[0]
fvars = fvars[1:]
'parameters': params
}).execute()
else:
- logger.info(expand_list(params, params["command"]))
+ if isinstance(params["command"][0], list):
+ for c in params["command"]:
+ logger.info(flatten(expand_item(params, c)))
+ else:
+ logger.info(flatten(expand_item(params, params["command"])))
else:
logger.error("parameter %s with value %s in task.foreach yielded no items" % (var, params[var]))
sys.exit(1)
else:
# This is the only task so taskp/jobp are the same
taskp = jobp
+except Exception as e:
+ logger.exception("caught exception")
+ logger.error("job parameters were:")
+ logger.error(pprint.pformat(jobp))
+ sys.exit(1)
+try:
if not args.dry_run:
if "task.vwd" in taskp:
# Populate output directory with symlinks to files in collection
if "task.cwd" in taskp:
os.chdir(subst.do_substitution(taskp, taskp["task.cwd"]))
- cmd = expand_list(taskp, taskp["command"])
+ cmd = []
+ if isinstance(taskp["command"][0], list):
+ for c in taskp["command"]:
+ cmd.append(flatten(expand_item(taskp, c)))
+ else:
+ cmd.append(flatten(expand_item(taskp, taskp["command"])))
- if not args.dry_run:
- if "task.stdin" in taskp:
- stdinname = subst.do_substitution(taskp, taskp["task.stdin"])
+ if "task.stdin" in taskp:
+ stdinname = subst.do_substitution(taskp, taskp["task.stdin"])
+ if not args.dry_run:
stdinfile = open(stdinname, "rb")
- if "task.stdout" in taskp:
- stdoutname = subst.do_substitution(taskp, taskp["task.stdout"])
+ if "task.stdout" in taskp:
+ stdoutname = subst.do_substitution(taskp, taskp["task.stdout"])
+ if not args.dry_run:
stdoutfile = open(stdoutname, "wb")
- logger.info("{}{}{}".format(' '.join(cmd), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else ""))
+ if "task.env" in taskp:
+ env = copy.copy(os.environ)
+ for k,v in taskp["task.env"].items():
+ env[k] = subst.do_substitution(taskp, v)
+ else:
+ env = None
+
+ logger.info("{}{}{}".format(' | '.join([' '.join(c) for c in cmd]), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else ""))
if args.dry_run:
sys.exit(0)
logger.error(pprint.pformat(taskp))
sys.exit(1)
+# rcode holds the return codes produced by each subprocess
+rcode = {}
try:
- sp = subprocess.Popen(cmd, shell=False, stdin=stdinfile, stdout=stdoutfile)
- sig = SigHandler()
+ subprocesses = []
+ close_streams = []
+ if stdinfile:
+ close_streams.append(stdinfile)
+ next_stdin = stdinfile
+
+ for i in xrange(len(cmd)):
+ if i == len(cmd)-1:
+ # this is the last command in the pipeline, so its stdout should go to stdoutfile
+ next_stdout = stdoutfile
+ else:
+ # this is an intermediate command in the pipeline, so its stdout should go to a pipe
+ next_stdout = subprocess.PIPE
+
+ sp = subprocess.Popen(cmd[i], shell=False, stdin=next_stdin, stdout=next_stdout, env=env)
+
+ # Need to close the FDs on our side so that subcommands will get SIGPIPE if the
+ # consuming process ends prematurely.
+ if sp.stdout:
+ close_streams.append(sp.stdout)
+
+ # Send this processes's stdout to to the next process's stdin
+ next_stdin = sp.stdout
+
+ subprocesses.append(sp)
+
+ # File descriptors have been handed off to the subprocesses, so close them here.
+ for s in close_streams:
+ s.close()
- # forward signals to the process.
- signal.signal(signal.SIGINT, lambda signum, frame: sig.send_signal(sp, signum))
- signal.signal(signal.SIGTERM, lambda signum, frame: sig.send_signal(sp, signum))
- signal.signal(signal.SIGQUIT, lambda signum, frame: sig.send_signal(sp, signum))
+ # Set up signal handling
+ sig = SigHandler()
- # wait for process to complete.
- rcode = sp.wait()
+ # Forward terminate signals to the subprocesses.
+ signal.signal(signal.SIGINT, lambda signum, frame: sig.send_signal(subprocesses, signum))
+ signal.signal(signal.SIGTERM, lambda signum, frame: sig.send_signal(subprocesses, signum))
+ signal.signal(signal.SIGQUIT, lambda signum, frame: sig.send_signal(subprocesses, signum))
+
+ active = 1
+ pids = set([s.pid for s in subprocesses])
+ while len(pids) > 0:
+ try:
+ (pid, status) = os.wait()
+ except OSError as e:
+ if e.errno == errno.EINTR:
+ pass
+ else:
+ raise
+ else:
+ pids.discard(pid)
+ if not taskp.get("task.ignore_rcode"):
+ rcode[pid] = (status >> 8)
+ else:
+ rcode[pid] = 0
if sig.sig is not None:
logger.critical("terminating on signal %s" % sig.sig)
sys.exit(2)
else:
- logger.info("completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
+ for i in xrange(len(cmd)):
+ r = rcode[subprocesses[i].pid]
+ logger.info("%s completed with exit code %i (%s)" % (cmd[i][0], r, "success" if r == 0 else "failed"))
except Exception as e:
logger.exception("caught exception")
signal.signal(signal.SIGTERM, signal.SIG_DFL)
signal.signal(signal.SIGQUIT, signal.SIG_DFL)
-for l in links:
- os.unlink(l)
-
logger.info("the following output files will be saved to keep:")
-subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"], stdout=sys.stderr)
+subprocess.call(["find", "-L", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"], stdout=sys.stderr, cwd=outdir)
logger.info("start writing output to keep")
-if "task.vwd" in taskp:
- if "task.foreach" in jobp:
- # This is a subtask, so don't merge with the original collection, that will happen at the end
- outcollection = vwd.checkin(subst.do_substitution(taskp, taskp["task.vwd"]), outdir, merge=False).manifest_text()
- else:
- # Just a single task, so do merge with the original collection
- outcollection = vwd.checkin(subst.do_substitution(taskp, taskp["task.vwd"]), outdir, merge=True).manifest_text()
-else:
- outcollection = robust_put.upload(outdir, logger)
+if "task.vwd" in taskp and "task.foreach" in jobp:
+ for root, dirs, files in os.walk(outdir):
+ for f in files:
+ s = os.lstat(os.path.join(root, f))
+ if stat.S_ISLNK(s.st_mode):
+ os.unlink(os.path.join(root, f))
+
+(outcollection, checkin_error) = vwd.checkin(outdir)
+
+# Success if we ran any subprocess, and they all exited 0.
+success = rcode and all(status == 0 for status in rcode.itervalues()) and not checkin_error
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
- 'output': outcollection,
- 'success': (rcode == 0),
+ 'output': outcollection.manifest_text(),
+ 'success': success,
'progress':1.0
}).execute()
-sys.exit(rcode)
+sys.exit(0 if success else 1)
projects / arvados.git / blobdiff