#!/usr/bin/env python
+import logging
+logging.basicConfig(level=logging.INFO, format="run-command: %(message)s")
+
import arvados
import re
import os
import subprocess
import sys
import shutil
-import subst
+import crunchutil.subst as subst
import time
import arvados.commands.put as put
import signal
import traceback
import pprint
import multiprocessing
-import logging
-import robust_put
-import vwd
+import crunchutil.robust_put as robust_put
+import crunchutil.vwd as vwd
os.umask(0077)
-logging.basicConfig(format="run-command: %(message)s")
t = arvados.current_task().tmpdir
fn = subst.do_substitution(p, value)
mode = os.stat(fn).st_mode
prefix = fn[len(os.environ['TASK_KEEPMOUNT'])+1:]
- if mode != None:
+ if mode is not None:
if stat.S_ISDIR(mode):
items = ["$(dir %s/%s/)" % (prefix, l) for l in os.listdir(fn)]
elif stat.S_ISREG(mode):
stdoutname = None
stdoutfile = None
+stdinname = None
+stdinfile = None
rcode = 1
try:
var = jobp["task.foreach"]
items = get_items(jobp, jobp[var])
logging.info("parallelizing on %s with items %s" % (var, items))
- if items != None:
+ if items is not None:
for i in items:
params = copy.copy(jobp)
params[var] = i
else:
taskp = jobp
- cmd = expand_list(taskp, taskp["command"])
-
if "task.vwd" in taskp:
# Populate output directory with symlinks to files in collection
vwd.checkout(subst.do_substitution(taskp, taskp["task.vwd"]), outdir)
- if "save.stdout" in taskp:
- stdoutname = subst.do_substitution(taskp, taskp["save.stdout"])
- stdoutfile = open(stdoutname, "wb")
-
if "task.cwd" in taskp:
os.chdir(subst.do_substitution(taskp, taskp["task.cwd"]))
- logging.info("{}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
+ cmd = expand_list(taskp, taskp["command"])
+
+ if "task.stdin" in taskp:
+ stdinname = subst.do_substitution(taskp, taskp["task.stdin"])
+ stdinfile = open(stdinname, "rb")
+
+ if "task.stdout" in taskp:
+ stdoutname = subst.do_substitution(taskp, taskp["task.stdout"])
+ stdoutfile = open(stdoutname, "wb")
+
+ logging.info("{}{}{}".format(' '.join(cmd), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else ""))
except Exception as e:
logging.exception("caught exception")
sys.exit(1)
try:
- sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile)
+ sp = subprocess.Popen(cmd, shell=False, stdin=stdinfile, stdout=stdoutfile)
sig = SigHandler()
# forward signals to the process.
# wait for process to complete.
rcode = sp.wait()
- if sig.sig != None:
+ if sig.sig is not None:
logging.critical("terminating on signal %s" % sig.sig)
sys.exit(2)
else: