X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/529a648458ceefc02d77abf470a2005a099d9907..c076dcc368300f5e767b6cb946551fd3c9c84a3b:/sdk/python/arvados/commands/run.py diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py index 7a298b4c17..ca51de1fe3 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 @@ -7,26 +27,45 @@ import json import re import os import stat -import put +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 + +from arvados._version import __version__ logger = logging.getLogger('arvados.arv-run') logger.setLevel(logging.INFO) arvrun_parser = argparse.ArgumentParser(parents=[arv_cmd.retry_opt]) -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-run-pipeline-instance") -arvrun_parser.add_argument('--docker-image', type=str, help="Docker image to use, otherwise use instance default.") -arvrun_parser.add_argument('--ignore-rcode', action="store_true", help="Commands that return non-zero return codes should not be considered failed.") -arvrun_parser.add_argument('--no-reuse', action="store_true", help="Do not reuse past jobs.") -arvrun_parser.add_argument('--no-wait', action="store_true", help="Do not wait and display logs after submitting command, just exit.") -arvrun_parser.add_argument('--project-uuid', type=str, help="Parent project of the pipeline") -arvrun_parser.add_argument('--git-dir', type=str, default="", help="Git repository passed to arv-crunch-job when using --local") -arvrun_parser.add_argument('--repository', type=str, default="arvados", help="repository field of component, default 'arvados'") -arvrun_parser.add_argument('--script-version', type=str, default="master", help="script_version field of component, default 'master'") +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-run-pipeline-instance") +arvrun_parser.add_argument('--docker-image', type=str, + help="Docker image to use, otherwise use instance default.") +arvrun_parser.add_argument('--ignore-rcode', action="store_true", + help="Commands that return non-zero return codes should not be considered failed.") +arvrun_parser.add_argument('--no-reuse', action="store_true", + help="Do not reuse past jobs.") +arvrun_parser.add_argument('--no-wait', action="store_true", + help="Do not wait and display logs after submitting command, just exit.") +arvrun_parser.add_argument('--project-uuid', type=str, + help="Parent project of the pipeline") +arvrun_parser.add_argument('--git-dir', type=str, default="", + help="Git repository passed to arv-crunch-job when using --local") +arvrun_parser.add_argument('--repository', type=str, default="arvados", + help="repository field of component, default 'arvados'") +arvrun_parser.add_argument('--script-version', type=str, default="master", + help="script_version field of component, default 'master'") +arvrun_parser.add_argument('--version', action='version', + version="%s %s" % (sys.argv[0], __version__), + help='Print version and exit.') arvrun_parser.add_argument('args', nargs=argparse.REMAINDER) class ArvFile(object): @@ -87,94 +126,138 @@ 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) - 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: + 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)) - else: - # trim leading '/' for path prefix test later - return UploadFile(prefix, absfn[1:]) - if stat.S_ISDIR(st.st_mode): - sp = os.path.split(absfn) - (pdh, branch) = is_in_collection(sp[0], sp[1]) - if pdh: + elif stat.S_ISDIR(st.st_mode): return ArvFile(prefix, dirPattern % (pdh, branch)) + else: + 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 uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None): +def write_file(collection, pathprefix, fn): + with open(os.path.join(pathprefix, fn)) as src: + dst = collection.open(fn, "w") + r = src.read(1024*128) + while r: + dst.write(r) + r = src.read(1024*128) + dst.close(flush=False) + +def uploadfiles(files, api, dry_run=False, num_retries=0, + project=None, + fnPattern="$(file %s/%s)", + name=None, + collection=None): # 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. - 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 + # until all file paths no longer have a common parent. + if files: + n = True + pathprefix = "/" + while n: + pathstep = None for c in files: - c.fn = c.fn[len(pathstep):] - - orgdir = os.getcwd() - os.chdir(pathprefix) - - 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.CollectionWriter(api, num_retries=num_retries) - stream = None + if collection is None: + collection = arvados.collection.Collection(api_client=api, num_retries=num_retries) + prev = "" for f in files: - sp = os.path.split(f.fn) - if sp[0] != stream: - stream = sp[0] - collection.start_new_stream(stream) - collection.write_file(f.fn, sp[1]) - - exists = api.collections().list(filters=[["owner_uuid", "=", project], - ["portable_data_hash", "=", collection.portable_data_hash()], - ["name", "=", name]]).execute(num_retries=num_retries) - if exists["items"]: - item = exists["items"][0] - logger.info("Using collection %s", item["uuid"]) + 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) + 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)) + + 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 else: - body = {"owner_uuid": project, "manifest_text": collection.manifest_text()} - if name is not None: - body["name"] = name - item = api.collections().create(body=body, ensure_unique_name=True).execute() - logger.info("Uploaded to %s", item["uuid"]) - - pdh = item["portable_data_hash"] + # empty collection + pdh = collection.portable_data_hash() + assert (pdh == config.EMPTY_BLOCK_LOCATOR), "Empty collection portable_data_hash did not have expected locator" + logger.info("Using empty collection %s", pdh) for c in files: + c.keepref = "%s/%s" % (pdh, c.fn) c.fn = fnPattern % (pdh, c.fn) - os.chdir(orgdir) - def main(arguments=None): args = arvrun_parser.parse_args(arguments) @@ -258,7 +341,7 @@ 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 = { @@ -278,8 +361,8 @@ 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:])