X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/77d9c05d89dabc9e9e9a15f46cd12c8ad61ed64e..cbf93e8d897448dbd52369afe89fef2392140ff1:/sdk/python/arvados/commands/run.py diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py index 46a56ca558..b17ed29180 100644 --- a/sdk/python/arvados/commands/run.py +++ b/sdk/python/arvados/commands/run.py @@ -1,5 +1,25 @@ -#!/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 @@ -7,7 +27,7 @@ import json import re import os import stat -import put +from . import put import time import subprocess import logging @@ -15,6 +35,7 @@ import sys import errno import arvados.commands._util as arv_cmd import arvados.collection +import arvados.config as config from arvados._version import __version__ @@ -105,7 +126,7 @@ def determine_project(root, current_user): # 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) @@ -122,62 +143,66 @@ def statfile(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"): # 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="$(file %s/%s)", - name=None): + name=None, + collection=None, + packed=True): # Find the smallest path prefix that includes all the files that need to be uploaded. # This starts at the root and iteratively removes common parent directory prefixes # until all file paths no longer have a common parent. - n = True - pathprefix = "/" - while n: - pathstep = None - for c in files: - if pathstep is None: - sp = c.fn.split('/') - if len(sp) < 2: - # no parent directories left - n = False - break - # path step takes next directory - pathstep = sp[0] + "/" - else: - # check if pathstep is common prefix for all files - if not c.fn.startswith(pathstep): - n = False - break - if n: - # pathstep is common parent directory for all files, so remove the prefix - # from each path - pathprefix += pathstep + if files: + n = True + pathprefix = "/" + while n: + pathstep = None for c in files: - c.fn = c.fn[len(pathstep):] - - logger.info("Upload local files: \"%s\"", '" "'.join([c.fn for c in files])) + if pathstep is None: + sp = c.fn.split('/') + if len(sp) < 2: + # no parent directories left + n = False + break + # path step takes next directory + pathstep = sp[0] + "/" + else: + # check if pathstep is common prefix for all files + if not c.fn.startswith(pathstep): + n = False + break + if n: + # pathstep is common parent directory for all files, so remove the prefix + # from each path + pathprefix += pathstep + for c in files: + c.fn = c.fn[len(pathstep):] + + logger.info("Upload local files: \"%s\"", '" "'.join([c.fn for c in files])) if dry_run: logger.info("$(input) is %s", pathprefix.rstrip('/')) pdh = "$(input)" else: files = sorted(files, key=lambda x: x.fn) - collection = arvados.collection.Collection(api_client=api, num_retries=num_retries) + 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) @@ -189,28 +214,55 @@ def uploadfiles(files, api, dry_run=False, num_retries=0, 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()], - ["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"]) + 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: - collection.save_new(name=name, owner_uuid=project, ensure_unique_name=True) + # 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.info("Using empty collection %s", pdh) for c in files: c.keepref = "%s/%s" % (pdh, c.fn) @@ -299,7 +351,7 @@ def main(arguments=None): if files: uploadfiles(files, api, dry_run=args.dry_run, num_retries=args.retries, project=project) - for i in xrange(1, len(slots)): + 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 = { @@ -319,8 +371,8 @@ def main(arguments=None): group_parser.add_argument('-b', '--batch-size', type=int) group_parser.add_argument('args', nargs=argparse.REMAINDER) - for s in xrange(2, len(slots)): - for i in xrange(0, len(slots[s])): + 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:])