-#!/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
+from . import put
import time
-#import arvados.command.ws as ws
import subprocess
import logging
+import sys
+import errno
+import arvados.commands._util as arv_cmd
+import arvados.collection
+import arvados.config as config
-logger = logging.getLogger('arvados.arv-run')
+from arvados._version import __version__
-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 directory to use to find run-command when using --local")
-arvrun_parser.add_argument('args', nargs=argparse.REMAINDER)
+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 __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):
- if root == "/":
+ try:
+ if root == "/":
+ return (None, None)
+ fn = os.path.join(root, ".arvados#collection")
+ if os.path.exists(fn):
+ with open(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)
- 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):
+# 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):
+ try:
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))
+ 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:
- # trim leading '/' for path prefix test later
- return UploadFile(prefix, absfn[1:])
+ raise Exception("%s is not a regular file or directory" % absfn)
+ else:
+ # 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
+
return prefix+fn
-def main(arguments=None):
- args = arvrun_parser.parse_args(arguments)
-
- reading_into = 2
-
- slots = [[], [], []]
- for c in args.args:
- if c == '>':
- reading_into = 0
- elif c == '<':
- reading_into = 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.
+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:
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 = "$(input)"
- else:
- pdh = put.main(["--portable-data-hash"]+[c.fn for c in files])
-
- for c in files:
- c.fn = "$(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": "3609-arv-run",
- "repository": "arvados",
- "script_parameters": {
- },
- "runtime_constraints": {
- "docker_image": args.docker_image
- }
- }
-
- task_foreach = []
- group_parser = argparse.ArgumentParser()
- group_parser.add_argument('--group', type=str)
- 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
- groupargs = group_parser.parse_args(slots[2][i+1:])
- component["script_parameters"][inp] = groupargs.args
- if groupargs.group:
- inpgroups = inp+"_groups"
- component["script_parameters"][inpgroups] = {"group":inp, "regex":groupargs.group}
- slots[s] = slots[s][0:i] + [{"foreach": inpgroups, "command": "$(%s)" % inpgroups}]
- task_foreach.append(inpgroups)
- else:
- slots[s] = slots[s][0:i] + ["$(%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"] = "$(stdin)"\
-
- if task_foreach:
- component["script_parameters"]["task.foreach"] = task_foreach
-
- component["script_parameters"]["command"] = slots[2:]
-
- pipeline = {
- "name": "",
- "components": {
- "command": component
- },
- "state":"RunningOnServer"
- }
-
- if args.dry_run:
- print(json.dumps(pipeline, indent=4))
- elif args.local:
- subprocess.call(["arv-crunch-job", "--job", json.dumps(component), "--git-dir", args.git_dir])
+ if dry_run:
+ logger.info("$(input) is %s", pathprefix.rstrip('/'))
+ pdh = "$(input)"
else:
- api = arvados.api('v1')
- pi = api.pipeline_instances().create(body=pipeline).execute()
- print "Running pipeline %s" % pi["uuid"]
- #ws.main(["--pipeline", pi["uuid"]])
+ 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.debug("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