X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/9bf790498c20c9f8ab9bffbf9c8e5311864bd91e..f7bf9d69603db2d500563648460e2a96524de266:/sdk/python/arvados/commands/run.py diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py index d8bb26e92e..0fe05da22b 100644 --- a/sdk/python/arvados/commands/run.py +++ b/sdk/python/arvados/commands/run.py @@ -1,3 +1,20 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# Copyright (C) 2018 Genome Research Ltd. +# +# SPDX-License-Identifier: Apache-2.0 +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + from __future__ import print_function from __future__ import absolute_import from builtins import range @@ -18,38 +35,13 @@ import sys import errno import arvados.commands._util as arv_cmd import arvados.collection +import arvados.config as config from arvados._version import __version__ logger = logging.getLogger('arvados.arv-run') logger.setLevel(logging.INFO) -arvrun_parser = argparse.ArgumentParser(parents=[arv_cmd.retry_opt]) -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-run-pipeline-instance") -arvrun_parser.add_argument('--docker-image', type=str, - help="Docker image to use, otherwise use instance default.") -arvrun_parser.add_argument('--ignore-rcode', action="store_true", - help="Commands that return non-zero return codes should not be considered failed.") -arvrun_parser.add_argument('--no-reuse', action="store_true", - help="Do not reuse past jobs.") -arvrun_parser.add_argument('--no-wait', action="store_true", - help="Do not wait and display logs after submitting command, just exit.") -arvrun_parser.add_argument('--project-uuid', type=str, - help="Parent project of the pipeline") -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('--version', action='version', - version="%s %s" % (sys.argv[0], __version__), - help='Print version and exit.') -arvrun_parser.add_argument('args', nargs=argparse.REMAINDER) - class ArvFile(object): def __init__(self, prefix, fn): self.prefix = prefix @@ -73,7 +65,7 @@ def is_in_collection(root, branch): return (None, None) fn = os.path.join(root, ".arvados#collection") if os.path.exists(fn): - with file(fn, 'r') as f: + with open(fn, 'r') as f: c = json.load(f) return (c["portable_data_hash"], branch) else: @@ -108,7 +100,7 @@ def determine_project(root, current_user): # ArvFile() (file already exists in a collection), UploadFile() (file needs to # be uploaded to a collection), or simply returns prefix+fn (which yields the # original parameter string). -def statfile(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"): +def statfile(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)", raiseOSError=False): absfn = os.path.abspath(fn) try: st = os.stat(absfn) @@ -125,62 +117,66 @@ def statfile(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"): # trim leading '/' for path prefix test later return UploadFile(prefix, absfn[1:]) except OSError as e: - if e.errno == errno.ENOENT: + if e.errno == errno.ENOENT and not raiseOSError: pass else: raise return prefix+fn -def write_file(collection, pathprefix, fn): - with open(os.path.join(pathprefix, fn)) as src: - dst = collection.open(fn, "w") +def write_file(collection, pathprefix, fn, flush=False): + with open(os.path.join(pathprefix, fn), "rb") as src: + dst = collection.open(fn, "wb") r = src.read(1024*128) while r: dst.write(r) r = src.read(1024*128) - dst.close(flush=False) + dst.close(flush=flush) def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", - name=None): + name=None, + collection=None, + packed=True): # Find the smallest path prefix that includes all the files that need to be uploaded. # This starts at the root and iteratively removes common parent directory prefixes # until all file paths no longer have a common parent. - n = True - pathprefix = "/" - while n: - pathstep = None - for c in files: - if pathstep is None: - sp = c.fn.split('/') - if len(sp) < 2: - # no parent directories left - n = False - break - # path step takes next directory - pathstep = sp[0] + "/" - else: - # check if pathstep is common prefix for all files - if not c.fn.startswith(pathstep): - n = False - break - if n: - # pathstep is common parent directory for all files, so remove the prefix - # from each path - pathprefix += pathstep + if files: + n = True + pathprefix = "/" + while n: + pathstep = None for c in files: - c.fn = c.fn[len(pathstep):] - - logger.info("Upload local files: \"%s\"", '" "'.join([c.fn for c in files])) + if pathstep is None: + sp = c.fn.split('/') + if len(sp) < 2: + # no parent directories left + n = False + break + # path step takes next directory + pathstep = sp[0] + "/" + else: + # check if pathstep is common prefix for all files + if not c.fn.startswith(pathstep): + n = False + break + if n: + # pathstep is common parent directory for all files, so remove the prefix + # from each path + pathprefix += pathstep + for c in files: + c.fn = c.fn[len(pathstep):] + + logger.info("Upload local files: \"%s\"", '" "'.join([c.fn for c in files])) if dry_run: logger.info("$(input) is %s", pathprefix.rstrip('/')) pdh = "$(input)" else: files = sorted(files, key=lambda x: x.fn) - collection = arvados.collection.Collection(api_client=api, num_retries=num_retries) + if collection is None: + collection = arvados.collection.Collection(api_client=api, num_retries=num_retries) prev = "" for f in files: localpath = os.path.join(pathprefix, f.fn) @@ -192,28 +188,55 @@ def uploadfiles(files, api, dry_run=False, num_retries=0, continue prev = localpath if os.path.isfile(localpath): - write_file(collection, pathprefix, f.fn) + write_file(collection, pathprefix, f.fn, not packed) elif os.path.isdir(localpath): for root, dirs, iterfiles in os.walk(localpath): root = root[len(pathprefix):] for src in iterfiles: - write_file(collection, pathprefix, os.path.join(root, src)) - - filters=[["portable_data_hash", "=", collection.portable_data_hash()], - ["name", "like", name+"%"]] - if project: - filters.append(["owner_uuid", "=", project]) - - exists = api.collections().list(filters=filters, limit=1).execute(num_retries=num_retries) - - if exists["items"]: - item = exists["items"][0] - pdh = item["portable_data_hash"] - logger.info("Using collection %s (%s)", pdh, item["uuid"]) + write_file(collection, pathprefix, os.path.join(root, src), not packed) + + pdh = None + if len(collection) > 0: + # non-empty collection + filters = [["portable_data_hash", "=", collection.portable_data_hash()]] + name_pdh = "%s (%s)" % (name, collection.portable_data_hash()) + if name: + filters.append(["name", "=", name_pdh]) + if project: + filters.append(["owner_uuid", "=", project]) + + # do the list / create in a loop with up to 2 tries as we are using `ensure_unique_name=False` + # and there is a potential race with other workflows that may have created the collection + # between when we list it and find it does not exist and when we attempt to create it. + tries = 2 + while pdh is None and tries > 0: + exists = api.collections().list(filters=filters, limit=1).execute(num_retries=num_retries) + + if exists["items"]: + item = exists["items"][0] + pdh = item["portable_data_hash"] + logger.info("Using collection %s (%s)", pdh, item["uuid"]) + else: + try: + collection.save_new(name=name_pdh, owner_uuid=project, ensure_unique_name=False) + pdh = collection.portable_data_hash() + logger.info("Uploaded to %s (%s)", pdh, collection.manifest_locator()) + except arvados.errors.ApiError as ae: + tries -= 1 + if pdh is None: + # Something weird going on here, probably a collection + # with a conflicting name but wrong PDH. We won't + # able to reuse it but we still need to save our + # collection, so so save it with unique name. + logger.info("Name conflict on '%s', existing collection has an unexpected portable data hash", name_pdh) + collection.save_new(name=name_pdh, owner_uuid=project, ensure_unique_name=True) + pdh = collection.portable_data_hash() + logger.info("Uploaded to %s (%s)", pdh, collection.manifest_locator()) else: - collection.save_new(name=name, owner_uuid=project, ensure_unique_name=True) + # empty collection pdh = collection.portable_data_hash() - logger.info("Uploaded to %s (%s)", pdh, collection.manifest_locator()) + assert (pdh == config.EMPTY_BLOCK_LOCATOR), "Empty collection portable_data_hash did not have expected locator, was %s" % pdh + logger.debug("Using empty collection %s", pdh) for c in files: c.keepref = "%s/%s" % (pdh, c.fn) @@ -221,164 +244,7 @@ def uploadfiles(files, api, dry_run=False, num_retries=0, 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") + raise Exception("Legacy arv-run removed.") if __name__ == '__main__': main()