X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/4f4ad25bf60751a09e316dca8c29cf3628ad7bdc..87c49a944230e400cb3529b30472e497d20912d6:/sdk/python/arvados/commands/run.py diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py index e27b3df79c..a45775470a 100644 --- a/sdk/python/arvados/commands/run.py +++ b/sdk/python/arvados/commands/run.py @@ -1,161 +1,250 @@ -#!/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()