import multiprocessing
import crunchutil.robust_put as robust_put
import crunchutil.vwd as vwd
+import argparse
+import json
+import tempfile
-os.umask(0077)
-
-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:
items = get_items(p, p[var])
params = copy.copy(p)
params[var] = items[int(c["index"])]
- r.extend(expand_list(params, c["command"]))
+ 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):
if isinstance(l, basestring):
- return [expand_item(p, l)]
+ return expand_item(p, l)
else:
return [exp for arg in l for exp in expand_item(p, arg)]
-def add_to_group(gr, match):
- m = ('^_^').join(match.groups())
- if m not in gr:
- gr[m] = []
- gr[m].append(match.group(0))
-
def get_items(p, value):
if isinstance(value, dict):
- if "regex" in value:
- pattern = re.compile(value["regex"])
- if "filter" in value:
- items = get_items(p, value["filter"])
- return [i for i in items if pattern.match(i)]
- elif "group" in value:
- items = get_items(p, value["group"])
- groups = {}
- for i in items:
- p = pattern.match(i)
- if p:
- add_to_group(groups, p)
- return [groups[k] for k in groups]
- elif "extract" in value:
- items = get_items(p, value["extract"])
- r = []
- for i in items:
- p = pattern.match(i)
- if p:
- r.append(p.groups())
- return r
+ 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.rstrip("\r\n") for line in f]
if len(fvars) > 0:
recursive_foreach(params, fvars)
else:
- 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()
+ 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:
if "task.foreach" in jobp:
- if arvados.current_task()['sequence'] == 0:
+ 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):
logger.error("value of task.foreach must be a string or non-empty list")
sys.exit(1)
recursive_foreach(jobp, jobp["task.foreach"])
- 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)
+ 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 "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")
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:")
projects / arvados.git / blobdiff