-#!/usr/bin/env python
-
+# 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
+from past.builtins import basestring
+from builtins import object
import arvados
+import arvados.commands.ws as ws
import argparse
import json
import re
import os
import stat
-import put
-import arvados.events
+from . import put
import time
+import subprocess
+import logging
+import sys
+import errno
+import arvados.commands._util as arv_cmd
+import arvados.collection
+import arvados.config as config
-arvrun_parser = argparse.ArgumentParser()
-arvrun_parser.add_argument('--dry-run', action="store_true")
-arvrun_parser.add_argument('--docker-image', type=str, default="arvados/jobs")
-arvrun_parser.add_argument('command')
-arvrun_parser.add_argument('args', nargs=argparse.REMAINDER)
+from arvados._version import __version__
-needupload_files = []
+logger = logging.getLogger('arvados.arv-run')
+logger.setLevel(logging.INFO)
class ArvFile(object):
def __init__(self, prefix, fn):
self.prefix = prefix
self.fn = fn
-def statfile(prefix, fn, pattern):
+ def __hash__(self):
+ return (self.prefix+self.fn).__hash__()
+
+ def __eq__(self, other):
+ return (self.prefix == other.prefix) and (self.fn == other.fn)
+
+class UploadFile(ArvFile):
+ pass
+
+# Determine if a file is in a collection, and return a tuple consisting of the
+# portable data hash and the path relative to the root of the collection.
+# Return None if the path isn't with an arv-mount collection or there was is error.
+def is_in_collection(root, branch):
+ try:
+ 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))
+ except (IOError, OSError):
+ return (None, None)
+
+# Determine the project to place the output of this command by searching upward
+# for arv-mount psuedofile indicating the project. If the cwd isn't within
+# an arv-mount project or there is an error, return current_user.
+def determine_project(root, current_user):
+ try:
+ if root == "/":
+ return current_user
+ fn = os.path.join(root, ".arvados#project")
+ if os.path.exists(fn):
+ with file(fn, 'r') as f:
+ c = json.load(f)
+ if 'writable_by' in c and current_user in c['writable_by']:
+ return c["uuid"]
+ else:
+ return current_user
+ else:
+ sp = os.path.split(root)
+ return determine_project(sp[0], current_user)
+ except (IOError, OSError):
+ return current_user
+
+# Determine if string corresponds to a file, and if that file is part of a
+# arv-mounted collection or only local to the machine. Returns one of
+# 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/)", raiseOSError=False):
absfn = os.path.abspath(fn)
- if os.path.exists(absfn):
- fn = os.path.abspath(fn)
- st = os.stat(fn)
- 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+"$(file "+c["portable_data_hash"]+"/" + os.path.basename(fn) + ")"
+ try:
+ st = os.stat(absfn)
+ sp = os.path.split(absfn)
+ (pdh, branch) = is_in_collection(sp[0], sp[1])
+ if pdh:
+ if stat.S_ISREG(st.st_mode):
+ return ArvFile(prefix, fnPattern % (pdh, branch))
+ elif stat.S_ISDIR(st.st_mode):
+ return ArvFile(prefix, dirPattern % (pdh, branch))
else:
- needupload_files.append(fn)
- return ArvFile(prefix, fn[1:])
- return prefix+fn
-
-def main(arguments=None):
- args = arvrun_parser.parse_args(arguments)
-
- patterns = [re.compile("(--[^=]+=)(.*)"),
- re.compile("(-[^=]+=)(.*)"),
- re.compile("(-.)(.+)")]
-
- commandargs = []
-
- for a in args.args:
- if a[0] == '-':
- matched = False
- for p in patterns:
- m = p.match(a)
- if m:
- commandargs.append(statfile(m.group(1), m.group(2), p))
- matched = True
- break
- if not matched:
- commandargs.append(a)
+ raise Exception("%s is not a regular file or directory" % absfn)
else:
- commandargs.append(statfile('', a, None))
+ # trim leading '/' for path prefix test later
+ return UploadFile(prefix, absfn[1:])
+ except OSError as e:
+ if e.errno == errno.ENOENT and not raiseOSError:
+ pass
+ else:
+ raise
- n = True
- pathprefix = "/"
- files = [c for c in commandargs if isinstance(c, ArvFile)]
- if len(files) > 0:
+ return prefix+fn
+
+def write_file(collection, pathprefix, fn, flush=False):
+ with open(os.path.join(pathprefix, fn), "rb") as src:
+ dst = collection.open(fn, "wb")
+ r = src.read(1024*128)
+ while r:
+ dst.write(r)
+ r = src.read(1024*128)
+ dst.close(flush=flush)
+
+def uploadfiles(files, api, dry_run=False, num_retries=0,
+ project=None,
+ fnPattern="$(file %s/%s)",
+ 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.
+ if files:
+ 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
for c in files:
c.fn = c.fn[len(pathstep):]
- os.chdir(pathprefix)
+ logger.info("Upload local files: \"%s\"", '" "'.join([c.fn for c in files]))
- if args.dry_run:
- print("cd %s" % pathprefix)
- print("arv-put \"%s\"" % '" "'.join([c.fn for c in files]))
- pdh = "$(input)"
- else:
- pdh = put.main(["--portable-data-hash"]+[c.fn for c in files])
-
- commandargs = [("%s$(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]
-
- component = {
- "script": "run-command",
- "script_version": "bf243e064a7a2ee4e69a87dc3ba46e949a545150",
- "repository": "arvados",
- "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]
-
- pipeline = {
- "name": "",
- "components": {
- args.command: component
- },
- "state":"RunningOnServer"
- }
-
- if args.dry_run:
- print(json.dumps(pipeline, indent=4))
+ if dry_run:
+ logger.info("$(input) is %s", pathprefix.rstrip('/'))
+ pdh = "$(input)"
else:
- api = arvados.api('v1')
- pi = api.pipeline_instances().create(body=pipeline).execute()
- ws = None
- def report(x):
- if "event_type" in x:
- print "\n"
- print x
- if x["event_type"] == "stderr":
- print x["properties"]["text"]
- elif x["event_type"] == "update" and x["properties"]["new_attributes"]["state"] in ["Complete", "Failed"]:
- ws.close_connection()
-
- ws = arvados.events.subscribe(api, [["object_uuid", "=", pi["uuid"]], ["event_type", "in", ["stderr", "update"]]], report)
- ws.run_forever()
+ files = sorted(files, key=lambda x: x.fn)
+ 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)
+ if prev and localpath.startswith(prev+"/"):
+ # If this path is inside an already uploaded subdirectory,
+ # don't redundantly re-upload it.
+ # e.g. we uploaded /tmp/foo and the next file is /tmp/foo/bar
+ # skip it because it starts with "/tmp/foo/"
+ continue
+ prev = localpath
+ if os.path.isfile(localpath):
+ 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), 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()
+ assert (pdh == config.EMPTY_BLOCK_LOCATOR), "Empty collection portable_data_hash did not have expected locator, was %s" % pdh
+ logger.info("Using empty collection %s", pdh)
+
+ for c in files:
+ c.keepref = "%s/%s" % (pdh, c.fn)
+ c.fn = fnPattern % (pdh, c.fn)
+
+
+def main(arguments=None):
+ raise Exception("Legacy arv-run removed.")
if __name__ == '__main__':
main()
projects / arvados.git / blobdiff