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 # Parse the command arguments into 'slots'. # All words following '>' are output arguments and are collected into slots[0]. # All words following '<' are input arguments and are collected into slots[1]. # slots[2..] store the parameters of each command in the pipeline. # # e.g. arv-run foo arg1 arg2 '|' bar arg3 arg4 '<' input1 input2 input3 '>' output.txt # will be parsed into: # [['output.txt'], # ['input1', 'input2', 'input3'], # ['foo', 'arg1', 'arg2'], # ['bar', 'arg3', 'arg4']] 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 if not args.dry_run: api = arvados.api('v1') if args.project_uuid: project = args.project_uuid else: project = determine_project(os.getcwd(), api.users().current().execute()["uuid"]) # Identify input files. Look at each parameter and test to see if there is # a file by that name. This uses 'patterns' to look for within # command line arguments, such as --foo=file.txt or -lfile.txt patterns = [re.compile("([^=]+=)(.*)"), re.compile("(-[A-Za-z])(.+)")] for j, command in enumerate(slots[1:]): for i, a in enumerate(command): if j > 0 and i == 0: # j == 0 is stdin, j > 0 is commands # always skip program executable (i == 0) in commands pass elif a.startswith('\\'): # if it starts with a \ then don't do any interpretation command[i] = a[1:] else: # See if it looks like a file command[i] = statfile('', a) # If a file named command[i] was found, it would now be an # ArvFile or UploadFile. If command[i] is a basestring, that # means it doesn't correspond exactly to a file, so do some # pattern matching. if isinstance(command[i], basestring): for p in patterns: m = p.match(a) if m: command[i] = statfile(m.group(1), m.group(2)) break files = [c for command in slots[1:] for c in command if isinstance(c, UploadFile)] if files: uploadfiles(files, api, dry_run=args.dry_run, num_retries=args.retries, project=project) for i in range(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": {} } if args.docker_image: component["runtime_constraints"]["docker_image"] = args.docker_image task_foreach = [] group_parser = argparse.ArgumentParser() group_parser.add_argument('-b', '--batch-size', type=int) group_parser.add_argument('args', nargs=argparse.REMAINDER) for s in range(2, len(slots)): for i in range(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] = {"value": {"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:] if args.ignore_rcode: component["script_parameters"]["task.ignore_rcode"] = args.ignore_rcode pipeline = { "name": "arv-run " + " | ".join([s[0] for s in slots[2:]]), "description": "@" + " ".join(starting_args) + "@", "components": { "command": component }, "state": "RunningOnClient" if args.local else "RunningOnServer" } if args.dry_run: print(json.dumps(pipeline, indent=4)) else: pipeline["owner_uuid"] = project pi = api.pipeline_instances().create(body=pipeline, ensure_unique_name=True).execute() logger.info("Running pipeline %s", pi["uuid"]) if args.local: subprocess.call(["arv-run-pipeline-instance", "--instance", pi["uuid"], "--run-jobs-here"] + (["--no-reuse"] if args.no_reuse else [])) elif not args.no_wait: ws.main(["--pipeline", pi["uuid"]]) pi = api.pipeline_instances().get(uuid=pi["uuid"]).execute() logger.info("Pipeline is %s", pi["state"]) if "output_uuid" in pi["components"]["command"]: logger.info("Output is %s", pi["components"]["command"]["output_uuid"]) else: logger.info("No output")
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 # Parse the command arguments into 'slots'. # All words following '>' are output arguments and are collected into slots[0]. # All words following '<' are input arguments and are collected into slots[1]. # slots[2..] store the parameters of each command in the pipeline. # # e.g. arv-run foo arg1 arg2 '|' bar arg3 arg4 '<' input1 input2 input3 '>' output.txt # will be parsed into: # [['output.txt'], # ['input1', 'input2', 'input3'], # ['foo', 'arg1', 'arg2'], # ['bar', 'arg3', 'arg4']] 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 if not args.dry_run: api = arvados.api('v1') if args.project_uuid: project = args.project_uuid else: project = determine_project( os.getcwd(), api.users().current().execute()["uuid"]) # Identify input files. Look at each parameter and test to see if there is # a file by that name. This uses 'patterns' to look for within # command line arguments, such as --foo=file.txt or -lfile.txt patterns = [re.compile("([^=]+=)(.*)"), re.compile("(-[A-Za-z])(.+)")] for j, command in enumerate(slots[1:]): for i, a in enumerate(command): if j > 0 and i == 0: # j == 0 is stdin, j > 0 is commands # always skip program executable (i == 0) in commands pass elif a.startswith('\\'): # if it starts with a \ then don't do any interpretation command[i] = a[1:] else: # See if it looks like a file command[i] = statfile('', a) # If a file named command[i] was found, it would now be an # ArvFile or UploadFile. If command[i] is a basestring, that # means it doesn't correspond exactly to a file, so do some # pattern matching. if isinstance(command[i], basestring): for p in patterns: m = p.match(a) if m: command[i] = statfile(m.group(1), m.group(2)) break files = [ c for command in slots[1:] for c in command if isinstance(c, UploadFile) ] if files: uploadfiles(files, api, dry_run=args.dry_run, num_retries=args.retries, project=project) 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": {} } if args.docker_image: component["runtime_constraints"]["docker_image"] = args.docker_image task_foreach = [] group_parser = argparse.ArgumentParser() group_parser.add_argument('-b', '--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] = { "value": { "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:] if args.ignore_rcode: component["script_parameters"]["task.ignore_rcode"] = args.ignore_rcode pipeline = { "name": "arv-run " + " | ".join([s[0] for s in slots[2:]]), "description": "@" + " ".join(starting_args) + "@", "components": { "command": component }, "state": "RunningOnClient" if args.local else "RunningOnServer" } if args.dry_run: print(json.dumps(pipeline, indent=4)) else: pipeline["owner_uuid"] = project pi = api.pipeline_instances().create( body=pipeline, ensure_unique_name=True).execute() logger.info("Running pipeline %s", pi["uuid"]) if args.local: subprocess.call([ "arv-run-pipeline-instance", "--instance", pi["uuid"], "--run-jobs-here" ] + (["--no-reuse"] if args.no_reuse else [])) elif not args.no_wait: ws.main(["--pipeline", pi["uuid"]]) pi = api.pipeline_instances().get(uuid=pi["uuid"]).execute() logger.info("Pipeline is %s", pi["state"]) if "output_uuid" in pi["components"]["command"]: logger.info("Output is %s", pi["components"]["command"]["output_uuid"]) else: logger.info("No output")
def run_ws(self, args): return arv_ws.main(args)
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 # Parse the command arguments into 'slots'. # All words following '>' are output arguments and are collected into slots[0]. # All words following '<' are input arguments and are collected into slots[1]. # slots[2..] store the parameters of each command in the pipeline. # # e.g. arv-run foo arg1 arg2 '|' bar arg3 arg4 '<' input1 input2 input3 '>' output.txt # will be parsed into: # [['output.txt'], # ['input1', 'input2', 'input3'], # ['foo', 'arg1', 'arg2'], # ['bar', 'arg3', 'arg4']] 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 if not args.dry_run: api = arvados.api('v1') if args.project_uuid: project = args.project_uuid else: project = determine_project(os.getcwd(), api.users().current().execute()["uuid"]) # Identify input files. Look at each parameter and test to see if there is # a file by that name. This uses 'patterns' to look for within # command line arguments, such as --foo=file.txt or -lfile.txt patterns = [re.compile("([^=]+=)(.*)"), re.compile("(-[A-Za-z])(.+)")] for j, command in enumerate(slots[1:]): for i, a in enumerate(command): if j > 0 and i == 0: # j == 0 is stdin, j > 0 is commands # always skip program executable (i == 0) in commands pass elif a.startswith('\\'): # if it starts with a \ then don't do any interpretation command[i] = a[1:] else: # See if it looks like a file command[i] = statfile('', a) # If a file named command[i] was found, it would now be an # ArvFile or UploadFile. If command[i] is a basestring, that # means it doesn't correspond exactly to a file, so do some # pattern matching. if isinstance(command[i], basestring): for p in patterns: m = p.match(a) if m: command[i] = statfile(m.group(1), m.group(2)) break 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):] orgdir = os.getcwd() os.chdir(pathprefix) print("Upload local files: \"%s\"" % '" "'.join([c.fn for c in files])) if args.dry_run: print("$(input) is %s" % pathprefix.rstrip('/')) pdh = "$(input)" else: files = sorted(files, key=lambda x: x.fn) collection = arvados.CollectionWriter(api, num_retries=args.retries) stream = None for f in files: sp = os.path.split(f.fn) if sp[0] != stream: stream = sp[0] collection.start_new_stream(stream) collection.write_file(f.fn, sp[1]) item = api.collections().create(body={"owner_uuid": project, "manifest_text": collection.manifest_text()}).execute() pdh = item["portable_data_hash"] print "Uploaded to %s" % item["uuid"] for c in files: c.fn = "$(file %s/%s)" % (pdh, c.fn) os.chdir(orgdir) for i in xrange(1, len(slots)): slots[i] = [("%s%s" % (c.prefix, c.fn)) if isinstance(c, ArvFile) else c for c in slots[i]] component = { "script": "run-command", "script_version": args.script_version, "repository": args.repository, "script_parameters": { }, "runtime_constraints": { "docker_image": args.docker_image } } task_foreach = [] group_parser = argparse.ArgumentParser() group_parser.add_argument('-b', '--batch-size', type=int) group_parser.add_argument('args', nargs=argparse.REMAINDER) for s in xrange(2, len(slots)): for i in xrange(0, len(slots[s])): if slots[s][i] == '--': inp = "input%i" % (s-2) groupargs = group_parser.parse_args(slots[2][i+1:]) if groupargs.batch_size: component["script_parameters"][inp] = {"value": {"batch":groupargs.args, "size":groupargs.batch_size}} slots[s] = slots[s][0:i] + [{"foreach": inp, "command": "$(%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:] if args.ignore_rcode: component["script_parameters"]["task.ignore_rcode"] = args.ignore_rcode pipeline = { "name": "arv-run " + " | ".join([s[0] for s in slots[2:]]), "description": "@" + " ".join(starting_args) + "@", "components": { "command": component }, "state": "RunningOnClient" if args.local else "RunningOnServer" } if args.dry_run: print(json.dumps(pipeline, indent=4)) else: pipeline["owner_uuid"] = project pi = api.pipeline_instances().create(body=pipeline, ensure_unique_name=True).execute() print "Running pipeline %s" % pi["uuid"] if args.local: subprocess.call(["arv-run-pipeline-instance", "--instance", pi["uuid"], "--run-jobs-here"] + (["--no-reuse"] if args.no_reuse else [])) elif not args.no_wait: ws.main(["--pipeline", pi["uuid"]]) pi = api.pipeline_instances().get(uuid=pi["uuid"]).execute() print "Pipeline is %s" % pi["state"] if "output_uuid" in pi["components"]["command"]: print "Output is %s" % pi["components"]["command"]["output_uuid"] else: print "No output"