#!/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 traceback
import pprint
import multiprocessing
-import logging
import crunchutil.robust_put as robust_put
import crunchutil.vwd as vwd
+import argparse
+import json
+import tempfile
-os.umask(0077)
-logging.basicConfig(format="run-command: %(message)s")
-
-t = arvados.current_task().tmpdir
+parser = argparse.ArgumentParser()
+parser.add_argument('--dry-run', action='store_true')
+parser.add_argument('--script-parameters', type=str, default="{}")
+args = parser.parse_args()
-api = arvados.api('v1')
+os.umask(0077)
-os.chdir(arvados.current_task().tmpdir)
-os.mkdir("tmpdir")
-os.mkdir("output")
+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("output")
+ os.chdir("output")
-outdir = os.getcwd()
+ outdir = os.getcwd()
-taskp = None
-jobp = arvados.current_job()['script_parameters']
-if len(arvados.current_task()['parameters']) > 0:
- taskp = 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:
+ 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 = []
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:
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, str) or isinstance(c, unicode):
+ elif isinstance(c, basestring):
return [subst.do_substitution(p, c)]
return []
def expand_list(p, l):
- return [exp for arg in l for exp in expand_item(p, arg)]
+ 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)
prefix = fn[len(os.environ['TASK_KEEPMOUNT'])+1:]
if mode is not None:
if stat.S_ISDIR(mode):
- items = ["$(dir %s/%s/)" % (prefix, l) for l in os.listdir(fn)]
+ items = [os.path.join(fn, l) for l in os.listdir(fn)]
elif stat.S_ISREG(mode):
with open(fn) as f:
- items = [line for line in f]
+ items = [line.rstrip("\r\n") for line in f]
return items
else:
return None
stdinfile = None
rcode = 1
-try:
- if "task.foreach" in jobp:
- if arvados.current_task()['sequence'] == 0:
- var = jobp["task.foreach"]
- items = get_items(jobp, jobp[var])
- logging.info("parallelizing on %s with items %s" % (var, items))
- if items is not None:
- for i in items:
- params = copy.copy(jobp)
- params[var] = i
+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()
+ }).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:
+ 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:
- # Base vwd collection will be merged with output fragments from
- # the other tasks by crunch.
+ # 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:
- sys.exit(1)
+ sys.exit(0)
else:
+ # This is the only task so taskp/jobp are the same
taskp = jobp
- 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 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"]))
+ if "task.cwd" in taskp:
+ os.chdir(subst.do_substitution(taskp, taskp["task.cwd"]))
cmd = expand_list(taskp, taskp["command"])
- if "task.stdin" in taskp:
- stdinname = subst.do_substitution(taskp, taskp["task.stdin"])
- stdinfile = open(stdinname, "rb")
+ 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")
+ 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 ""))
+ 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:
- logging.exception("caught exception")
- logging.error("task parameters was:")
- logging.error(pprint.pformat(taskp))
+ logger.exception("caught exception")
+ logger.error("task parameters were:")
+ logger.error(pprint.pformat(taskp))
sys.exit(1)
try:
rcode = sp.wait()
if sig.sig is not None:
- logging.critical("terminating on signal %s" % sig.sig)
+ logger.critical("terminating on signal %s" % sig.sig)
sys.exit(2)
else:
- logging.info("completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
+ logger.info("completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
except Exception as e:
- logging.exception("caught exception")
+ logger.exception("caught exception")
# restore default signal handlers.
signal.signal(signal.SIGINT, signal.SIG_DFL)
for l in links:
os.unlink(l)
-logging.info("the following output files will be saved to keep:")
+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)
-logging.info("start writing output to keep")
+logger.info("start writing output to keep")
if "task.vwd" in taskp:
if "task.foreach" in jobp:
# 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)
+ outcollection = robust_put.upload(outdir, logger)
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
projects / arvados.git / blobdiff