X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c0cead2ee16700cf14baba7993297e83787aedbb..cf4c25824e15e3b9a7c1439ab3aff17d8be52630:/sdk/python/arvados/commands/run.py diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py index 97278c8087..1e64eeb1da 100644 --- a/sdk/python/arvados/commands/run.py +++ b/sdk/python/arvados/commands/run.py @@ -1,105 +1,150 @@ -#!/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") -arvrun_parser.add_argument('--local', action="store_true") -arvrun_parser.add_argument('--docker-image', type=str, default="arvados/jobs") -arvrun_parser.add_argument('--git-dir', type=str, default="") -arvrun_parser.add_argument('args', nargs=argparse.REMAINDER) +logger = logging.getLogger('arvados.arv-run') +logger.setLevel(logging.INFO) -class UploadFile(object): +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 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) - 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 "%s$(file %s/%s)" % (prefix, 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: @@ -123,58 +168,83 @@ def main(arguments=None): 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 = "$(input)" - else: - pdh = put.main(["--portable-data-hash"]+[c.fn for c in files]) - - for i in xrange(1, len(slots)): - slots[i] = [("%s$(file %s/%s)" % (c.prefix, pdh, c.fn)) if isinstance(c, UploadFile) else c for c in slots[i]] - - component = { - "script": "run-command", - "script_version": "3609-arv-run", - "repository": "arvados", - "script_parameters": { - "command": slots[2:] - }, - "runtime_constraints": { - "docker_image": args.docker_image - } - } - - task_foreach = [] - - 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"] = "$(stdin)"\ - - if task_foreach: - component["script_parameters"]["task.foreach"] = task_foreach - - pipeline = { - "name": "", - "components": { - "command": component - }, - "state":"RunningOnServer" - } - - if args.dry_run: - print(json.dumps(pipeline, indent=4)) - elif args.local: - subprocess.call(["arv-crunch-job", "--job", json.dumps(component), "--git-dir", args.git_dir]) + if dry_run: + logger.info("$(input) is %s", pathprefix.rstrip('/')) + pdh = "$(input)" else: - api = arvados.api('v1') - pi = api.pipeline_instances().create(body=pipeline).execute() - #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()