X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/0fdfa049801418ecd1faf33ec1415f3b689ea761..fa541df794b486efa220bd83bb119e87cca8e2de:/sdk/python/arvados/commands/run.py diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py index 9df0a84d82..2375f5831e 100644 --- a/sdk/python/arvados/commands/run.py +++ b/sdk/python/arvados/commands/run.py @@ -8,81 +8,132 @@ import os import stat import put import time -#import arvados.command.ws as ws +import arvados.commands.ws as ws import subprocess +import logging + +logger = logging.getLogger('arvados.arv-run') arvrun_parser = argparse.ArgumentParser() -arvrun_parser.add_argument('--dry-run', action="store_true") -arvrun_parser.add_argument('--local', action="store_true") -arvrun_parser.add_argument('--docker-image', type=str, default="arvados/jobs") -arvrun_parser.add_argument('--git-dir', type=str, default="") -arvrun_parser.add_argument('command') +arvrun_parser.add_argument('--dry-run', action="store_true", help="Print out the pipeline that would be submitted and exit") +arvrun_parser.add_argument('--local', action="store_true", help="Run locally using arv-crunch-job") +arvrun_parser.add_argument('--docker-image', type=str, default="arvados/jobs", help="Docker image to use, default arvados/jobs") +arvrun_parser.add_argument('--git-dir', type=str, default="", help="Git repository passed to arv-crunch-job when using --local") +arvrun_parser.add_argument('--repository', type=str, default="arvados", help="repository field of component, default 'arvados'") +arvrun_parser.add_argument('--script-version', type=str, default="master", help="script_version field of component, default 'master'") arvrun_parser.add_argument('args', nargs=argparse.REMAINDER) -needupload_files = [] - class ArvFile(object): def __init__(self, prefix, fn): self.prefix = prefix self.fn = fn -def statfile(prefix, fn, pattern): +class UploadFile(ArvFile): + pass + +def is_in_collection(root, branch): + if root == "/": + return (None, None) + fn = os.path.join(root, ".arvados#collection") + if os.path.exists(fn): + with file(fn, 'r') as f: + c = json.load(f) + return (c["portable_data_hash"], branch) + else: + sp = os.path.split(root) + return is_in_collection(sp[0], os.path.join(sp[1], branch)) + +def statfile(prefix, fn): absfn = os.path.abspath(fn) if os.path.exists(absfn): - fn = os.path.abspath(fn) - st = os.stat(fn) + st = os.stat(absfn) if stat.S_ISREG(st.st_mode): - mount = os.path.dirname(fn)+"/.arvados#collection" - if os.path.exists(mount): - with file(mount, 'r') as f: - c = json.load(f) - return prefix+"$(file "+c["portable_data_hash"]+"/" + os.path.basename(fn) + ")" + sp = os.path.split(absfn) + (pdh, branch) = is_in_collection(sp[0], sp[1]) + if pdh: + return ArvFile(prefix, "$(file %s/%s)" % (pdh, branch)) else: - needupload_files.append(fn) - return ArvFile(prefix, fn[1:]) + # trim leading '/' for path prefix test later + return UploadFile(prefix, absfn[1:]) return prefix+fn def main(arguments=None): args = arvrun_parser.parse_args(arguments) + if len(args.args) == 0: + arvrun_parser.print_help() + return + + starting_args = args.args + + reading_into = 2 + + slots = [[], [], []] + for c in args.args: + if c.startswith('>'): + reading_into = 0 + if len(c) > 1: + slots[reading_into].append(c[1:]) + elif c.startswith('<'): + reading_into = 1 + if len(c) > 1: + slots[reading_into].append(c[1:]) + elif c == '|': + reading_into = len(slots) + slots.append([]) + else: + slots[reading_into].append(c) + + if slots[0] and len(slots[0]) > 1: + logger.error("Can only specify a single stdout file (run-command substitutions are permitted)") + return + patterns = [re.compile("(--[^=]+=)(.*)"), re.compile("(-[^=]+=)(.*)"), re.compile("(-.)(.+)")] - commandargs = [] - - for a in args.args: - if a[0] == '-': - matched = False - for p in patterns: - m = p.match(a) - if m: - commandargs.append(statfile(m.group(1), m.group(2), p)) - matched = True - break - if not matched: - commandargs.append(a) - else: - commandargs.append(statfile('', a, None)) + for command in slots[1:]: + for i in xrange(0, len(command)): + a = command[i] + if a[0] == '-': + # parameter starts with '-' so it might be a command line + # parameter with a file name, do some pattern matching + matched = False + for p in patterns: + m = p.match(a) + if m: + command[i] = statfile(m.group(1), m.group(2)) + break + else: + # parameter might be a file, so test it + command[i] = statfile('', a) n = True pathprefix = "/" - files = [c for c in commandargs if isinstance(c, ArvFile)] + files = [c for command in slots[1:] for c in command if isinstance(c, UploadFile)] if len(files) > 0: + # Find the smallest path prefix that includes all the files that need to be uploaded. + # This starts at the root and iteratively removes common parent directory prefixes + # until all file pathes no longer have a common parent. while n: pathstep = None for c in files: if pathstep is None: sp = c.fn.split('/') if len(sp) < 2: + # no parent directories left n = False break + # path step takes next directory pathstep = sp[0] + "/" else: + # check if pathstep is common prefix for all files if not c.fn.startswith(pathstep): n = False break if n: + # pathstep is common parent directory for all files, so remove the prefix + # from each path pathprefix += pathstep for c in files: c.fn = c.fn[len(pathstep):] @@ -96,48 +147,61 @@ def main(arguments=None): else: pdh = put.main(["--portable-data-hash"]+[c.fn for c in files]) - commandargs = [("%s$(file %s/%s)" % (c.prefix, pdh, c.fn)) if isinstance(c, ArvFile) else c for c in commandargs] - - cut = None - i = -1 - stdio = [None, None] - for j in xrange(0, len(commandargs)): - c = commandargs[j] - if c == '<': - stdio[0] = [] - i = 0 - cut = j if cut is None else cut - elif c == '>': - stdio[1] = [] - i = 1 - cut = j if cut is None else cut - elif i > -1: - stdio[i].append(c) - - if cut is not None: - commandargs = commandargs[:cut] + for c in files: + c.fn = "$(file %s/%s)" % (pdh, c.fn) + + for i in xrange(1, len(slots)): + slots[i] = [("%s%s" % (c.prefix, c.fn)) if isinstance(c, ArvFile) else c for c in slots[i]] component = { "script": "run-command", - "script_version": "4f4ad25bf60751a09e316dca8c29cf3628ad7bdc", - "repository": "arvados", + "script_version": args.script_version, + "repository": args.repository, "script_parameters": { - "command": [args.command]+commandargs }, "runtime_constraints": { "docker_image": args.docker_image } } - if stdio[0]: - component["script_parameters"]["task.stdin"] = stdio[0][0] - if stdio[1]: - component["script_parameters"]["task.stdout"] = stdio[1][0] + task_foreach = [] + group_parser = argparse.ArgumentParser() + group_parser.add_argument('--batch-size', type=int) + group_parser.add_argument('args', nargs=argparse.REMAINDER) + + for s in xrange(2, len(slots)): + for i in xrange(0, len(slots[s])): + if slots[s][i] == '--': + inp = "input%i" % (s-2) + groupargs = group_parser.parse_args(slots[2][i+1:]) + if groupargs.batch_size: + component["script_parameters"][inp] = {"batch":groupargs.args, "size":groupargs.batch_size} + slots[s] = slots[s][0:i] + [{"foreach": inp, "command": "$(%s)" % inp}] + else: + component["script_parameters"][inp] = groupargs.args + slots[s] = slots[s][0:i] + ["$(%s)" % inp] + task_foreach.append(inp) + break + if slots[s][i] == '\--': + slots[s][i] = '--' + + if slots[0]: + component["script_parameters"]["task.stdout"] = slots[0][0] + if slots[1]: + task_foreach.append("stdin") + component["script_parameters"]["stdin"] = slots[1] + component["script_parameters"]["task.stdin"] = "$(stdin)"\ + + if task_foreach: + component["script_parameters"]["task.foreach"] = task_foreach + + component["script_parameters"]["command"] = slots[2:] pipeline = { - "name": "", + "name": " | ".join([s[0] for s in slots[2:]]), + "description": "@" + " ".join(starting_args) + "@", "components": { - args.command: component + "command": component }, "state":"RunningOnServer" } @@ -149,7 +213,8 @@ def main(arguments=None): else: api = arvados.api('v1') pi = api.pipeline_instances().create(body=pipeline).execute() - #ws.main(["--pipeline", pi["uuid"]]) + print "Running pipeline %s" % pi["uuid"] + ws.main(["--pipeline", pi["uuid"]]) if __name__ == '__main__': main()