+# 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
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
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:
# 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)
# 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,
- collection=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.
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()]]
- if name:
- filters.append(["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"])
- elif len(collection) > 0:
- collection.save_new(name=name, owner_uuid=project, ensure_unique_name=True)
+ 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:
+ # 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)
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()
projects / arvados.git / blobdiff