#!/usr/bin/env python
+import logging
+
+logger = logging.getLogger('run-command')
+log_handler = logging.StreamHandler()
+log_handler.setFormatter(logging.Formatter("run-command: %(message)s"))
+logger.addHandler(log_handler)
+logger.setLevel(logging.INFO)
+
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 stat
+import copy
+import traceback
+import pprint
+import multiprocessing
+import crunchutil.robust_put as robust_put
+import crunchutil.vwd as vwd
+import argparse
+import json
+import tempfile
-os.umask(0077)
+parser = argparse.ArgumentParser()
+parser.add_argument('--dry-run', action='store_true')
+parser.add_argument('--script-parameters', type=str, default="{}")
+args = parser.parse_args()
-t = arvados.current_task().tmpdir
+os.umask(0077)
-api = arvados.api('v1')
+if not args.dry_run:
+ api = arvados.api('v1')
+ t = arvados.current_task().tmpdir
+ os.chdir(arvados.current_task().tmpdir)
+ os.mkdir("tmpdir")
+ os.mkdir("output")
-os.chdir(arvados.current_task().tmpdir)
-os.mkdir("tmpdir")
-os.mkdir("output")
+ os.chdir("output")
-os.chdir("output")
+ outdir = os.getcwd()
-if len(arvados.current_task()['parameters']) > 0:
- p = arvados.current_task()['parameters']
+ taskp = None
+ jobp = arvados.current_job()['script_parameters']
+ if len(arvados.current_task()['parameters']) > 0:
+ taskp = arvados.current_task()['parameters']
else:
- p = arvados.current_job()['script_parameters']
+ outdir = "/tmp"
+ jobp = json.loads(args.job_parameters)
+ os.environ['JOB_UUID'] = 'zzzzz-8i9sb-1234567890abcde'
+ os.environ['TASK_UUID'] = 'zzzzz-ot0gb-1234567890abcde'
+ os.environ['CRUNCH_SRC'] = '/tmp/crunche-src'
+ if 'TASK_KEEPMOUNT' not in os.environ:
+ os.environ['TASK_KEEPMOUNT'] = '/keep'
links = []
-def sub_link(v):
- r = os.path.basename(v)
- os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r)
- links.append(r)
- return r
-
def sub_tmpdir(v):
return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
+def sub_outdir(v):
+ return outdir
+
def sub_cores(v):
- return os.environ['CRUNCH_NODE_SLOTS']
+ return str(multiprocessing.cpu_count())
+
+def sub_jobid(v):
+ return os.environ['JOB_UUID']
+
+def sub_taskid(v):
+ return os.environ['TASK_UUID']
+
+def sub_jobsrc(v):
+ return os.environ['CRUNCH_SRC']
-subst.default_subs["link "] = sub_link
-subst.default_subs["tmpdir"] = sub_tmpdir
+subst.default_subs["task.tmpdir"] = sub_tmpdir
+subst.default_subs["task.outdir"] = sub_outdir
+subst.default_subs["job.srcdir"] = sub_jobsrc
subst.default_subs["node.cores"] = sub_cores
+subst.default_subs["job.uuid"] = sub_jobid
+subst.default_subs["task.uuid"] = sub_taskid
+
+class SigHandler(object):
+ def __init__(self):
+ self.sig = None
+
+ def send_signal(self, sp, signum):
+ sp.send_signal(signum)
+ self.sig = signum
+
+def add_to_group(gr, match):
+ m = match.groups()
+ if m not in gr:
+ gr[m] = []
+ gr[m].append(match.group(0))
+
+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])
+ r = []
+ for i in items:
+ params = copy.copy(p)
+ params[var] = i
+ r.extend(expand_list(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])
+ params = copy.copy(p)
+ params[var] = items[int(c["index"])]
+ return expand_list(params, c["command"])
+ if "regex" in c:
+ pattern = re.compile(c["regex"])
+ if "filter" in c:
+ items = get_items(p, p[c["filter"]])
+ return [i for i in items if pattern.match(i)]
+ elif "group" in c:
+ items = get_items(p, p[c["group"]])
+ groups = {}
+ for i in items:
+ 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"]])
+ r = []
+ for i in items:
+ match = pattern.match(i)
+ if match:
+ r.append(list(match.groups()))
+ return r
+ elif isinstance(c, list):
+ return expand_list(p, 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)
+ else:
+ return [exp for arg in l for exp in expand_item(p, arg)]
+
+def get_items(p, value):
+ if isinstance(value, dict):
+ return 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
+stdoutname = None
+stdoutfile = None
+stdinname = None
+stdinfile = None
rcode = 1
+def recursive_foreach(params, fvars):
+ var = fvars[0]
+ fvars = fvars[1:]
+ items = get_items(params, params[var])
+ logger.info("parallelizing on %s with items %s" % (var, items))
+ if items is not None:
+ for i in items:
+ params = copy.copy(params)
+ params[var] = i
+ if len(fvars) > 0:
+ recursive_foreach(params, fvars)
+ else:
+ if not args.dry_run:
+ arvados.api().job_tasks().create(body={
+ 'job_uuid': arvados.current_job()['uuid'],
+ 'created_by_job_task_uuid': arvados.current_task()['uuid'],
+ 'sequence': 1,
+ 'parameters': params
+ }).execute()
+ else:
+ logger.info(expand_list(params, params["command"]))
+ else:
+ logger.error("parameter %s with value %s in task.foreach yielded no items" % (var, params[var]))
+ sys.exit(1)
+
try:
- cmd = []
- for c in p["command"]:
- cmd.append(subst.do_substitution(p, c))
+ if "task.foreach" in jobp:
+ if args.dry_run or arvados.current_task()['sequence'] == 0:
+ # This is the first task to start the other tasks and exit
+ fvars = jobp["task.foreach"]
+ if isinstance(fvars, basestring):
+ fvars = [fvars]
+ if not isinstance(fvars, list) or len(fvars) == 0:
+ logger.error("value of task.foreach must be a string or non-empty list")
+ sys.exit(1)
+ recursive_foreach(jobp, jobp["task.foreach"])
+ if not args.dry_run:
+ if "task.vwd" in jobp:
+ # Set output of the first task to the base vwd collection so it
+ # will be merged with output fragments from the other tasks by
+ # crunch.
+ arvados.current_task().set_output(subst.do_substitution(jobp, jobp["task.vwd"]))
+ else:
+ arvados.current_task().set_output(None)
+ sys.exit(0)
+ else:
+ # This is the only task so taskp/jobp are the same
+ taskp = jobp
+
+ if not args.dry_run:
+ 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 "task.cwd" in taskp:
+ os.chdir(subst.do_substitution(taskp, taskp["task.cwd"]))
+
+ cmd = expand_list(taskp, taskp["command"])
+
+ if not args.dry_run:
+ 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")
+
+ logger.info("{}{}{}".format(' '.join(cmd), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else ""))
+
+ if args.dry_run:
+ sys.exit(0)
+except subst.SubstitutionError as e:
+ logger.error(str(e))
+ logger.error("task parameters were:")
+ logger.error(pprint.pformat(taskp))
+ sys.exit(1)
+except Exception as e:
+ logger.exception("caught exception")
+ logger.error("task parameters were:")
+ logger.error(pprint.pformat(taskp))
+ sys.exit(1)
- stdoutname = None
- stdoutfile = None
- if "stdout" in p:
- stdoutname = subst.do_substitution(p, p["stdout"])
- stdoutfile = open(stdoutname, "wb")
+try:
+ sp = subprocess.Popen(cmd, shell=False, stdin=stdinfile, stdout=stdoutfile)
+ sig = SigHandler()
- print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
+ # 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))
- rcode = subprocess.call(cmd, stdout=stdoutfile)
+ # wait for process to complete.
+ rcode = sp.wait()
- print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
+ 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"))
except Exception as e:
- print("run-command: caught exception: {}".format(e))
-
-finally:
- for l in links:
- os.unlink(l)
-
- print("run-command: the follow output files will be saved to keep:")
-
- subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"])
-
- print("run-command: start writing output to keep")
-
- done = False
- while not done:
- try:
- out = arvados.CollectionWriter()
- out.write_directory_tree(".", max_manifest_depth=0)
- outuuid = out.finish()
- api.job_tasks().update(uuid=arvados.current_task()['uuid'],
- body={
- 'output':outuuid,
- 'success': (rcode == 0),
- 'progress':1.0
- }).execute()
- done = True
- except Exception as e:
- print("run-command: caught exception: {}".format(e))
- time.sleep(5)
+ logger.exception("caught exception")
+
+# restore default signal handlers.
+signal.signal(signal.SIGINT, signal.SIG_DFL)
+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)
+
+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)
+
+api.job_tasks().update(uuid=arvados.current_task()['uuid'],
+ body={
+ 'output': outcollection,
+ 'success': (rcode == 0),
+ 'progress':1.0
+ }).execute()
sys.exit(rcode)
projects / arvados.git / blobdiff