#!/usr/bin/env python import arvados import argparse import json import re import os import stat import put import time 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", 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) class ArvFile(object): def __init__(self, prefix, fn): self.prefix = prefix self.fn = fn 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): st = os.stat(absfn) if stat.S_ISREG(st.st_mode): 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: # 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("(-.)(.+)")] 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 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):] os.chdir(pathprefix) if args.dry_run: print("cd %s" % pathprefix) print("arv-put \"%s\"" % '" "'.join([c.fn for c in files])) pdh = "$(input)" else: pdh = put.main(["--portable-data-hash"]+[c.fn for c in files]) for c in files: c.fn = "$(file %s/%s)" % (pdh, c.fn) for i in xrange(1, len(slots)): slots[i] = [("%s%s" % (c.prefix, c.fn)) if isinstance(c, ArvFile) else c for c in slots[i]] component = { "script": "run-command", "script_version": args.script_version, "repository": args.repository, "script_parameters": { }, "runtime_constraints": { "docker_image": args.docker_image } } task_foreach = [] group_parser = argparse.ArgumentParser() group_parser.add_argument('--batch-size', type=int) group_parser.add_argument('args', nargs=argparse.REMAINDER) for s in xrange(2, len(slots)): for i in xrange(0, len(slots[s])): if slots[s][i] == '--': inp = "input%i" % (s-2) groupargs = group_parser.parse_args(slots[2][i+1:]) if groupargs.batch_size: component["script_parameters"][inp] = {"batch":groupargs.args, "size":groupargs.batch_size} slots[s] = slots[s][0:i] + [{"foreach": inp, "command": "$(%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": " ".join(starting_args), "components": { "command": component }, "state":"RunningOnServer" } if args.dry_run: print(json.dumps(pipeline, indent=4)) elif args.local: subprocess.call(["arv-crunch-job", "--job", json.dumps(component), "--git-dir", args.git_dir]) else: api = arvados.api('v1') pi = api.pipeline_instances().create(body=pipeline).execute() print "Running pipeline %s" % pi["uuid"] ws.main(["--pipeline", pi["uuid"]]) if __name__ == '__main__': main()