X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d81ea65da05119d5c6480d373b5d42bbee8ae1ad..b14bc80d764b85a6ddfed32198b2144b5adf2637:/crunch_scripts/run-command diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command index c624e3cadf..c1e7475060 100755 --- a/crunch_scripts/run-command +++ b/crunch_scripts/run-command @@ -1,7 +1,12 @@ #!/usr/bin/env python import logging -logging.basicConfig(level=logging.INFO, format="run-command: %(message)s") + +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 @@ -20,25 +25,40 @@ 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) - -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 = [] @@ -75,6 +95,12 @@ class SigHandler(object): 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: @@ -86,17 +112,50 @@ def expand_item(p, 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) @@ -105,10 +164,10 @@ def get_items(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 @@ -119,58 +178,87 @@ stdinname = 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: @@ -186,13 +274,13 @@ 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) @@ -202,11 +290,11 @@ signal.signal(signal.SIGQUIT, 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: @@ -216,7 +304,7 @@ if "task.vwd" in taskp: # 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={