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"])
elif isinstance(c, list):
return expand_list(p, c)
elif isinstance(c, str) or isinstance(c, unicode):
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 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
+
if isinstance(value, list):
return expand_list(p, value)
items = ["$(dir %s/%s/)" % (prefix, 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
+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:
+ 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.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:
- var = jobp["task.foreach"]
- items = get_items(jobp, jobp[var])
- logger.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
- 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 "task.vwd" in jobp:
- # Base vwd collection 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 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 "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:
projects / arvados.git / blobdiff