X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/2fe1e71c5cc17dbf06fd7b1e188fd0279c07d3ca..72007cdcdcc228f1ba04b6963fdd9864b30bf281:/crunch_scripts/run-command diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command index fc3134f651..74793d4fce 100755 --- a/crunch_scripts/run-command +++ b/crunch_scripts/run-command @@ -57,12 +57,10 @@ else: jobp = json.loads(args.script_parameters) os.environ['JOB_UUID'] = 'zzzzz-8i9sb-1234567890abcde' os.environ['TASK_UUID'] = 'zzzzz-ot0gb-1234567890abcde' - os.environ['CRUNCH_SRC'] = '/tmp/crunche-src' + os.environ['CRUNCH_SRC'] = '/tmp/crunch-src' if 'TASK_KEEPMOUNT' not in os.environ: os.environ['TASK_KEEPMOUNT'] = '/keep' -links = [] - def sub_tmpdir(v): return os.path.join(arvados.current_task().tmpdir, 'tmpdir') @@ -156,6 +154,8 @@ def var_items(p, c, key): def expand_item(p, c): if isinstance(c, dict): if "foreach" in c and "command" in c: + # Expand a command template for each item in the specified user + # parameter var, items = var_items(p, c, "foreach") if var is None: raise EvaluationError("Must specify 'var' in foreach") @@ -166,6 +166,7 @@ def expand_item(p, c): r.append(expand_item(params, c["command"])) return r elif "list" in c and "index" in c and "command" in c: + # extract a single item from a list var, items = var_items(p, c, "list") if var is None: raise EvaluationError("Must specify 'var' in list") @@ -175,9 +176,13 @@ def expand_item(p, c): elif "regex" in c: pattern = re.compile(c["regex"]) if "filter" in c: + # filter list so that it only includes items that match a + # regular expression _, items = var_items(p, c, "filter") return [i for i in items if pattern.match(i)] elif "group" in c: + # generate a list of lists, where items are grouped on common + # subexpression match _, items = var_items(p, c, "group") groups = {} for i in items: @@ -186,6 +191,8 @@ def expand_item(p, c): add_to_group(groups, match) return [groups[k] for k in groups] elif "extract" in c: + # generate a list of lists, where items are split by + # subexpression match _, items = var_items(p, c, "extract") r = [] for i in items: @@ -194,6 +201,7 @@ def expand_item(p, c): r.append(list(match.groups())) return r elif "batch" in c and "size" in c: + # generate a list of lists, where items are split into a batch size _, items = var_items(p, c, "batch") sz = int(c["size"]) r = [] @@ -209,8 +217,8 @@ def expand_item(p, c): return expand_item(p, p[m.group(1)]) else: return subst.do_substitution(p, c) - - raise EvaluationError("expand_item() unexpected parameter type %s" % (type(c)) + else: + raise EvaluationError("expand_item() unexpected parameter type %s" % type(c)) # Evaluate in a list context # "p" is the parameter scope, "value" will be evaluated @@ -323,6 +331,13 @@ try: if not args.dry_run: stdoutfile = open(stdoutname, "wb") + if "task.env" in taskp: + env = copy.copy(os.environ) + for k,v in taskp["task.env"].items(): + env[k] = subst.do_substitution(taskp, v) + else: + env = None + logger.info("{}{}{}".format(' | '.join([' '.join(c) for c in cmd]), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else "")) if args.dry_run: @@ -338,6 +353,8 @@ except Exception as e: logger.error(pprint.pformat(taskp)) sys.exit(1) +# rcode holds the return codes produced by each subprocess +rcode = {} try: subprocesses = [] close_streams = [] @@ -353,7 +370,7 @@ try: # this is an intermediate command in the pipeline, so its stdout should go to a pipe next_stdout = subprocess.PIPE - sp = subprocess.Popen(cmd[i], shell=False, stdin=next_stdin, stdout=next_stdout) + sp = subprocess.Popen(cmd[i], shell=False, stdin=next_stdin, stdout=next_stdout, env=env) # Need to close the FDs on our side so that subcommands will get SIGPIPE if the # consuming process ends prematurely. @@ -379,14 +396,20 @@ try: active = 1 pids = set([s.pid for s in subprocesses]) - rcode = {} while len(pids) > 0: - (pid, status) = os.wait() - pids.discard(pid) - if not taskp.get("task.ignore_rcode"): - rcode[pid] = (status >> 8) + try: + (pid, status) = os.wait() + except OSError as e: + if e.errno == errno.EINTR: + pass + else: + raise else: - rcode[pid] = 0 + pids.discard(pid) + if not taskp.get("task.ignore_rcode"): + rcode[pid] = (status >> 8) + else: + rcode[pid] = 0 if sig.sig is not None: logger.critical("terminating on signal %s" % sig.sig) @@ -404,33 +427,29 @@ 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) +subprocess.call(["find", "-L", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"], stdout=sys.stderr, cwd=outdir) 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) +if "task.vwd" in taskp and "task.foreach" in jobp: + for root, dirs, files in os.walk(outdir): + for f in files: + s = os.lstat(os.path.join(root, f)) + if stat.S_ISLNK(s.st_mode): + os.unlink(os.path.join(root, f)) + +(outcollection, checkin_error) = vwd.checkin(outdir) -# Success if no non-zero return codes -success = not any([status != 0 for status in rcode.values()]) +# Success if we ran any subprocess, and they all exited 0. +success = rcode and all(status == 0 for status in rcode.itervalues()) and not checkin_error api.job_tasks().update(uuid=arvados.current_task()['uuid'], body={ - 'output': outcollection, + 'output': outcollection.manifest_text(), 'success': success, 'progress':1.0 }).execute() -sys.exit(rcode) +sys.exit(0 if success else 1)