X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/31d31c010bb6b5170e3962fdd50c6d393cfe6076..055b9792b7692d6c42f4e13d38dc6cd008396a6f:/sdk/python/arvados/commands/put.py diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py index 7ee77fd147..f6f85ba696 100644 --- a/sdk/python/arvados/commands/put.py +++ b/sdk/python/arvados/commands/put.py @@ -1,3 +1,7 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + from __future__ import division from future.utils import listitems, listvalues from builtins import str @@ -6,10 +10,12 @@ import argparse import arvados import arvados.collection import base64 +import ciso8601 import copy import datetime import errno import fcntl +import fnmatch import hashlib import json import logging @@ -26,10 +32,10 @@ import traceback from apiclient import errors as apiclient_errors from arvados._version import __version__ +from arvados.util import keep_locator_pattern import arvados.commands._util as arv_cmd -CAUGHT_SIGNALS = [signal.SIGINT, signal.SIGQUIT, signal.SIGTERM] api_client = None upload_opts = argparse.ArgumentParser(add_help=False) @@ -39,7 +45,9 @@ upload_opts.add_argument('--version', action='version', help='Print version and exit.') upload_opts.add_argument('paths', metavar='path', type=str, nargs='*', help=""" -Local file or directory. Default: read from standard input. +Local file or directory. If path is a directory reference with a trailing +slash, then just upload the directory's contents; otherwise upload the +directory itself. Default: read from standard input. """) _group = upload_opts.add_mutually_exclusive_group() @@ -69,8 +77,7 @@ Synonym for --stream. _group.add_argument('--stream', action='store_true', help=""" Store the file content and display the resulting manifest on -stdout. Do not write the manifest to Keep or save a Collection object -in Arvados. +stdout. Do not save a Collection object in Arvados. """) _group.add_argument('--as-manifest', action='store_true', dest='manifest', @@ -134,6 +141,10 @@ physical storage devices (e.g., disks) should have a copy of each data block. Default is to use the server-provided default (if any) or 2. """) +upload_opts.add_argument('--storage-classes', help=""" +Specify comma separated list of storage classes to be used when saving data to Keep. +""") + upload_opts.add_argument('--threads', type=int, metavar='N', default=None, help=""" Set the number of upload threads to be used. Take into account that @@ -143,6 +154,30 @@ On high latency installations, using a greater number will improve overall throughput. """) +upload_opts.add_argument('--exclude', metavar='PATTERN', default=[], + action='append', help=""" +Exclude files and directories whose names match the given glob pattern. When +using a path-like pattern like 'subdir/*.txt', all text files inside 'subdir' +directory, relative to the provided input dirs will be excluded. +When using a filename pattern like '*.txt', any text file will be excluded +no matter where it is placed. +For the special case of needing to exclude only files or dirs directly below +the given input directory, you can use a pattern like './exclude_this.gif'. +You can specify multiple patterns by using this argument more than once. +""") + +_group = upload_opts.add_mutually_exclusive_group() +_group.add_argument('--follow-links', action='store_true', default=True, + dest='follow_links', help=""" +Follow file and directory symlinks (default). +""") +_group.add_argument('--no-follow-links', action='store_false', dest='follow_links', + help=""" +Ignore file and directory symlinks. Even paths given explicitly on the +command line will be skipped if they are symlinks. +""") + + run_opts = argparse.ArgumentParser(add_help=False) run_opts.add_argument('--project-uuid', metavar='UUID', help=""" @@ -174,6 +209,18 @@ Display machine-readable progress on stderr (bytes and, if known, total data size). """) +run_opts.add_argument('--silent', action='store_true', + help=""" +Do not print any debug messages to console. (Any error messages will +still be displayed.) +""") + +run_opts.add_argument('--batch', action='store_true', default=False, + help=""" +Retries with '--no-resume --no-cache' if cached state contains invalid/expired +block signatures. +""") + _group = run_opts.add_mutually_exclusive_group() _group.add_argument('--resume', action='store_true', default=True, help=""" @@ -194,6 +241,19 @@ _group.add_argument('--no-cache', action='store_false', dest='use_cache', Do not save upload state in a cache file for resuming. """) +_group = upload_opts.add_mutually_exclusive_group() +_group.add_argument('--trash-at', metavar='YYYY-MM-DDTHH:MM', default=None, + help=""" +Set the trash date of the resulting collection to an absolute date in the future. +The accepted format is defined by the ISO 8601 standard. Examples: 20090103, 2009-01-03, 20090103T181505, 2009-01-03T18:15:05.\n +Timezone information can be added. If not, the provided date/time is assumed as being in the local system's timezone. +""") +_group.add_argument('--trash-after', type=int, metavar='DAYS', default=None, + help=""" +Set the trash date of the resulting collection to an amount of days from the +date/time that the upload process finishes. +""") + arg_parser = argparse.ArgumentParser( description='Copy data from the local filesystem to Keep.', parents=[upload_opts, run_opts, arv_cmd.retry_opt]) @@ -206,15 +266,14 @@ def parse_arguments(arguments): args.paths = ["-" if x == "/dev/stdin" else x for x in args.paths] - if len(args.paths) != 1 or os.path.isdir(args.paths[0]): - if args.filename: - arg_parser.error(""" + if args.filename and (len(args.paths) != 1 or os.path.isdir(args.paths[0])): + arg_parser.error(""" --filename argument cannot be used when storing a directory or multiple files. """) # Turn on --progress by default if stderr is a tty. - if (not (args.batch_progress or args.no_progress) + if (not (args.batch_progress or args.no_progress or args.silent) and os.isatty(sys.stderr.fileno())): args.progress = True @@ -232,9 +291,17 @@ def parse_arguments(arguments): if not args.filename: args.filename = 'stdin' + # Remove possible duplicated patterns + if len(args.exclude) > 0: + args.exclude = list(set(args.exclude)) + return args +class PathDoesNotExistError(Exception): + pass + + class CollectionUpdateError(Exception): pass @@ -243,6 +310,9 @@ class ResumeCacheConflict(Exception): pass +class ResumeCacheInvalidError(Exception): + pass + class ArvPutArgumentConflict(Exception): pass @@ -266,6 +336,24 @@ class FileUploadList(list): super(FileUploadList, self).append(other) +# Appends the X-Request-Id to the log message when log level is ERROR or DEBUG +class ArvPutLogFormatter(logging.Formatter): + std_fmtr = logging.Formatter(arvados.log_format, arvados.log_date_format) + err_fmtr = None + request_id_informed = False + + def __init__(self, request_id): + self.err_fmtr = logging.Formatter( + arvados.log_format+' (X-Request-Id: {})'.format(request_id), + arvados.log_date_format) + + def format(self, record): + if (not self.request_id_informed) and (record.levelno in (logging.DEBUG, logging.ERROR)): + self.request_id_informed = True + return self.err_fmtr.format(record) + return self.std_fmtr.format(record) + + class ResumeCache(object): CACHE_DIR = '.cache/arvados/arv-put' @@ -292,7 +380,7 @@ class ResumeCache(object): try: fcntl.flock(fileobj, fcntl.LOCK_EX | fcntl.LOCK_NB) except IOError: - raise ResumeCacheConflict("{} locked".format(fileobj.name)) + raise ResumeCacheConflict(u"{} locked".format(fileobj.name)) def load(self): self.cache_file.seek(0) @@ -323,7 +411,7 @@ class ResumeCache(object): new_cache = os.fdopen(new_cache_fd, 'r+') json.dump(data, new_cache) os.rename(new_cache_name, self.filename) - except (IOError, OSError, ResumeCacheConflict) as error: + except (IOError, OSError, ResumeCacheConflict): try: os.unlink(new_cache_name) except NameError: # mkstemp failed. @@ -356,17 +444,22 @@ class ArvPutUploadJob(object): } def __init__(self, paths, resume=True, use_cache=True, reporter=None, - bytes_expected=None, name=None, owner_uuid=None, + name=None, owner_uuid=None, api_client=None, batch_mode=False, ensure_unique_name=False, num_retries=None, - put_threads=None, replication_desired=None, - filename=None, update_time=60.0, update_collection=None, - logger=logging.getLogger('arvados.arv_put'), dry_run=False): + put_threads=None, replication_desired=None, filename=None, + update_time=60.0, update_collection=None, storage_classes=None, + logger=logging.getLogger('arvados.arv_put'), dry_run=False, + follow_links=True, exclude_paths=[], exclude_names=None, + trash_at=None): self.paths = paths self.resume = resume self.use_cache = use_cache + self.batch_mode = batch_mode self.update = False self.reporter = reporter - self.bytes_expected = bytes_expected + # This will set to 0 before start counting, if no special files are going + # to be read. + self.bytes_expected = None self.bytes_written = 0 self.bytes_skipped = 0 self.name = name @@ -376,6 +469,8 @@ class ArvPutUploadJob(object): self.replication_desired = replication_desired self.put_threads = put_threads self.filename = filename + self.storage_classes = storage_classes + self._api_client = api_client self._state_lock = threading.Lock() self._state = None # Previous run state (file list & manifest) self._current_files = [] # Current run file list @@ -393,6 +488,16 @@ class ArvPutUploadJob(object): self.logger = logger self.dry_run = dry_run self._checkpoint_before_quit = True + self.follow_links = follow_links + self.exclude_paths = exclude_paths + self.exclude_names = exclude_names + self._trash_at = trash_at + + if self._trash_at is not None: + if type(self._trash_at) not in [datetime.datetime, datetime.timedelta]: + raise TypeError('trash_at should be None, timezone-naive datetime or timedelta') + if type(self._trash_at) == datetime.datetime and self._trash_at.tzinfo is not None: + raise TypeError('provided trash_at datetime should be timezone-naive') if not self.use_cache and self.resume: raise ArvPutArgumentConflict('resume cannot be True when use_cache is False') @@ -404,45 +509,104 @@ class ArvPutUploadJob(object): # Load cached data if any and if needed self._setup_state(update_collection) + # Build the upload file list, excluding requested files and counting the + # bytes expected to be uploaded. + self._build_upload_list() + + def _build_upload_list(self): + """ + Scan the requested paths to count file sizes, excluding requested files + and dirs and building the upload file list. + """ + # If there aren't special files to be read, reset total bytes count to zero + # to start counting. + if not any([p for p in self.paths + if not (os.path.isfile(p) or os.path.isdir(p))]): + self.bytes_expected = 0 + + for path in self.paths: + # Test for stdin first, in case some file named '-' exist + if path == '-': + if self.dry_run: + raise ArvPutUploadIsPending() + self._write_stdin(self.filename or 'stdin') + elif not os.path.exists(path): + raise PathDoesNotExistError(u"file or directory '{}' does not exist.".format(path)) + elif (not self.follow_links) and os.path.islink(path): + self.logger.warning("Skipping symlink '{}'".format(path)) + continue + elif os.path.isdir(path): + # Use absolute paths on cache index so CWD doesn't interfere + # with the caching logic. + orig_path = path + path = os.path.abspath(path) + if orig_path[-1:] == os.sep: + # When passing a directory reference with a trailing slash, + # its contents should be uploaded directly to the + # collection's root. + prefixdir = path + else: + # When passing a directory reference with no trailing slash, + # upload the directory to the collection's root. + prefixdir = os.path.dirname(path) + prefixdir += os.sep + for root, dirs, files in os.walk(path, + followlinks=self.follow_links): + root_relpath = os.path.relpath(root, path) + if root_relpath == '.': + root_relpath = '' + # Exclude files/dirs by full path matching pattern + if self.exclude_paths: + dirs[:] = [d for d in dirs + if not any(pathname_match( + os.path.join(root_relpath, d), pat) + for pat in self.exclude_paths)] + files = [f for f in files + if not any(pathname_match( + os.path.join(root_relpath, f), pat) + for pat in self.exclude_paths)] + # Exclude files/dirs by name matching pattern + if self.exclude_names is not None: + dirs[:] = [d for d in dirs + if not self.exclude_names.match(d)] + files = [f for f in files + if not self.exclude_names.match(f)] + # Make os.walk()'s dir traversing order deterministic + dirs.sort() + files.sort() + for f in files: + filepath = os.path.join(root, f) + # Add its size to the total bytes count (if applicable) + if self.follow_links or (not os.path.islink(filepath)): + if self.bytes_expected is not None: + self.bytes_expected += os.path.getsize(filepath) + self._check_file(filepath, + os.path.join(root[len(prefixdir):], f)) + else: + filepath = os.path.abspath(path) + # Add its size to the total bytes count (if applicable) + if self.follow_links or (not os.path.islink(filepath)): + if self.bytes_expected is not None: + self.bytes_expected += os.path.getsize(filepath) + self._check_file(filepath, + self.filename or os.path.basename(path)) + # If dry-mode is on, and got up to this point, then we should notify that + # there aren't any file to upload. + if self.dry_run: + raise ArvPutUploadNotPending() + # Remove local_collection's files that don't exist locally anymore, so the + # bytes_written count is correct. + for f in self.collection_file_paths(self._local_collection, + path_prefix=""): + if f != 'stdin' and f != self.filename and not f in self._file_paths: + self._local_collection.remove(f) + def start(self, save_collection): """ Start supporting thread & file uploading """ - if not self.dry_run: - self._checkpointer.start() + self._checkpointer.start() try: - for path in self.paths: - # Test for stdin first, in case some file named '-' exist - if path == '-': - if self.dry_run: - raise ArvPutUploadIsPending() - self._write_stdin(self.filename or 'stdin') - elif os.path.isdir(path): - # Use absolute paths on cache index so CWD doesn't interfere - # with the caching logic. - prefixdir = path = os.path.abspath(path) - if prefixdir != '/': - prefixdir += '/' - for root, dirs, files in os.walk(path): - # Make os.walk()'s dir traversing order deterministic - dirs.sort() - files.sort() - for f in files: - self._check_file(os.path.join(root, f), - os.path.join(root[len(prefixdir):], f)) - else: - self._check_file(os.path.abspath(path), - self.filename or os.path.basename(path)) - # If dry-mode is on, and got up to this point, then we should notify that - # there aren't any file to upload. - if self.dry_run: - raise ArvPutUploadNotPending() - # Remove local_collection's files that don't exist locally anymore, so the - # bytes_written count is correct. - for f in self.collection_file_paths(self._local_collection, - path_prefix=""): - if f != 'stdin' and f != self.filename and not f in self._file_paths: - self._local_collection.remove(f) # Update bytes_written from current local collection and # report initial progress. self._update() @@ -452,10 +616,14 @@ class ArvPutUploadJob(object): except (SystemExit, Exception) as e: self._checkpoint_before_quit = False # Log stack trace only when Ctrl-C isn't pressed (SIGINT) - # Note: We're expecting SystemExit instead of KeyboardInterrupt because - # we have a custom signal handler in place that raises SystemExit with - # the catched signal's code. - if not isinstance(e, SystemExit) or e.code != -2: + # Note: We're expecting SystemExit instead of + # KeyboardInterrupt because we have a custom signal + # handler in place that raises SystemExit with the catched + # signal's code. + if isinstance(e, PathDoesNotExistError): + # We aren't interested in the traceback for this case + pass + elif not isinstance(e, SystemExit) or e.code != -2: self.logger.warning("Abnormal termination:\n{}".format( traceback.format_exc())) raise @@ -473,6 +641,17 @@ class ArvPutUploadJob(object): if self.use_cache: self._cache_file.close() + def _collection_trash_at(self): + """ + Returns the trash date that the collection should use at save time. + Takes into account absolute/relative trash_at values requested + by the user. + """ + if type(self._trash_at) == datetime.timedelta: + # Get an absolute datetime for trash_at + return datetime.datetime.utcnow() + self._trash_at + return self._trash_at + def save_collection(self): if self.update: # Check if files should be updated on the remote collection. @@ -487,12 +666,17 @@ class ArvPutUploadJob(object): else: # The file already exist on remote collection, skip it. pass - self._remote_collection.save(num_retries=self.num_retries) + self._remote_collection.save(num_retries=self.num_retries, + trash_at=self._collection_trash_at()) else: + if len(self._local_collection) == 0: + self.logger.warning("No files were uploaded, skipping collection creation.") + return self._local_collection.save_new( name=self.name, owner_uuid=self.owner_uuid, ensure_unique_name=self.ensure_unique_name, - num_retries=self.num_retries) + num_retries=self.num_retries, + trash_at=self._collection_trash_at()) def destroy_cache(self): if self.use_cache: @@ -547,6 +731,15 @@ class ArvPutUploadJob(object): self._save_state() except Exception as e: self.logger.error("Unexpected error trying to save cache file: {}".format(e)) + # Keep remote collection's trash_at attribute synced when using relative expire dates + if self._remote_collection is not None and type(self._trash_at) == datetime.timedelta: + try: + self._api_client.collections().update( + uuid=self._remote_collection.manifest_locator(), + body={'trash_at': self._collection_trash_at().strftime("%Y-%m-%dT%H:%M:%S.%fZ")} + ).execute(num_retries=self.num_retries) + except Exception as e: + self.logger.error("Unexpected error trying to update remote collection's expire date: {}".format(e)) else: self.bytes_written = self.bytes_skipped # Call the reporter, if any @@ -558,11 +751,16 @@ class ArvPutUploadJob(object): def _write_stdin(self, filename): output = self._local_collection.open(filename, 'wb') - self._write(sys.stdin, output) + self._write(sys.stdin.buffer, output) output.close() def _check_file(self, source, filename): - """Check if this file needs to be uploaded""" + """ + Check if this file needs to be uploaded + """ + # Ignore symlinks when requested + if (not self.follow_links) and os.path.islink(source): + return resume_offset = 0 should_upload = False new_file_in_cache = False @@ -597,6 +795,7 @@ class ArvPutUploadJob(object): elif file_in_local_collection.permission_expired(): # Permission token expired, re-upload file. This will change whenever # we have a API for refreshing tokens. + self.logger.warning(u"Uploaded file '{}' access token expired, will re-upload it from scratch".format(filename)) should_upload = True self._local_collection.remove(filename) elif cached_file_data['size'] == file_in_local_collection.size(): @@ -611,7 +810,7 @@ class ArvPutUploadJob(object): # Inconsistent cache, re-upload the file should_upload = True self._local_collection.remove(filename) - self.logger.warning("Uploaded version of file '{}' is bigger than local version, will re-upload it from scratch.".format(source)) + self.logger.warning(u"Uploaded version of file '{}' is bigger than local version, will re-upload it from scratch.".format(source)) # Local file differs from cached data, re-upload it. else: if file_in_local_collection: @@ -619,7 +818,13 @@ class ArvPutUploadJob(object): should_upload = True if should_upload: - self._files_to_upload.append((source, resume_offset, filename)) + try: + self._files_to_upload.append((source, resume_offset, filename)) + except ArvPutUploadIsPending: + # This could happen when running on dry-mode, close cache file to + # avoid locking issues. + self._cache_file.close() + raise def _upload_files(self): for source, resume_offset, filename in self._files_to_upload: @@ -647,6 +852,20 @@ class ArvPutUploadJob(object): def _my_collection(self): return self._remote_collection if self.update else self._local_collection + def _get_cache_filepath(self): + # Set up cache file name from input paths. + md5 = hashlib.md5() + md5.update(arvados.config.get('ARVADOS_API_HOST', '!nohost').encode()) + realpaths = sorted(os.path.realpath(path) for path in self.paths) + md5.update(b'\0'.join([p.encode() for p in realpaths])) + if self.filename: + md5.update(self.filename.encode()) + cache_filename = md5.hexdigest() + cache_filepath = os.path.join( + arv_cmd.make_home_conf_dir(self.CACHE_DIR, 0o700, 'raise'), + cache_filename) + return cache_filepath + def _setup_state(self, update_collection): """ Create a new cache file or load a previously existing one. @@ -655,7 +874,11 @@ class ArvPutUploadJob(object): if update_collection and re.match(arvados.util.collection_uuid_pattern, update_collection): try: - self._remote_collection = arvados.collection.Collection(update_collection) + self._remote_collection = arvados.collection.Collection( + update_collection, + api_client=self._api_client, + storage_classes_desired=self.storage_classes, + num_retries=self.num_retries) except arvados.errors.ApiError as error: raise CollectionUpdateError("Cannot read collection {} ({})".format(update_collection, error)) else: @@ -665,23 +888,13 @@ class ArvPutUploadJob(object): raise CollectionUpdateError("Collection locator unknown: '{}'".format(update_collection)) if self.use_cache: - # Set up cache file name from input paths. - md5 = hashlib.md5() - md5.update(arvados.config.get('ARVADOS_API_HOST', '!nohost').encode()) - realpaths = sorted(os.path.realpath(path) for path in self.paths) - md5.update(b'\0'.join([p.encode() for p in realpaths])) - if self.filename: - md5.update(self.filename.encode()) - cache_filename = md5.hexdigest() - cache_filepath = os.path.join( - arv_cmd.make_home_conf_dir(self.CACHE_DIR, 0o700, 'raise'), - cache_filename) + cache_filepath = self._get_cache_filepath() if self.resume and os.path.exists(cache_filepath): - self.logger.info("Resuming upload from cache file {}".format(cache_filepath)) + self.logger.info(u"Resuming upload from cache file {}".format(cache_filepath)) self._cache_file = open(cache_filepath, 'a+') else: # --no-resume means start with a empty cache file. - self.logger.info("Creating new cache file at {}".format(cache_filepath)) + self.logger.info(u"Creating new cache file at {}".format(cache_filepath)) self._cache_file = open(cache_filepath, 'w+') self._cache_filename = self._cache_file.name self._lock_file(self._cache_file) @@ -701,8 +914,63 @@ class ArvPutUploadJob(object): self.logger.info("No cache usage requested for this run.") # No cache file, set empty state self._state = copy.deepcopy(self.EMPTY_STATE) + if not self._cached_manifest_valid(): + if not self.batch_mode: + raise ResumeCacheInvalidError() + else: + self.logger.info("Invalid signatures on cache file '{}' while being run in 'batch mode' -- continuing anyways.".format(self._cache_file.name)) + self.use_cache = False # Don't overwrite preexisting cache file. + self._state = copy.deepcopy(self.EMPTY_STATE) # Load the previous manifest so we can check if files were modified remotely. - self._local_collection = arvados.collection.Collection(self._state['manifest'], replication_desired=self.replication_desired, put_threads=self.put_threads) + self._local_collection = arvados.collection.Collection( + self._state['manifest'], + replication_desired=self.replication_desired, + storage_classes_desired=self.storage_classes, + put_threads=self.put_threads, + api_client=self._api_client, + num_retries=self.num_retries) + + def _cached_manifest_valid(self): + """ + Validate the oldest non-expired block signature to check if cached manifest + is usable: checking if the cached manifest was not created with a different + arvados account. + """ + if self._state.get('manifest', None) is None: + # No cached manifest yet, all good. + return True + now = datetime.datetime.utcnow() + oldest_exp = None + oldest_loc = None + block_found = False + for m in keep_locator_pattern.finditer(self._state['manifest']): + loc = m.group(0) + try: + exp = datetime.datetime.utcfromtimestamp(int(loc.split('@')[1], 16)) + except IndexError: + # Locator without signature + continue + block_found = True + if exp > now and (oldest_exp is None or exp < oldest_exp): + oldest_exp = exp + oldest_loc = loc + if not block_found: + # No block signatures found => no invalid block signatures. + return True + if oldest_loc is None: + # Locator signatures found, but all have expired. + # Reset the cache and move on. + self.logger.info('Cache expired, starting from scratch.') + self._state['manifest'] = '' + return True + kc = arvados.KeepClient(api_client=self._api_client, + num_retries=self.num_retries) + try: + kc.head(oldest_loc) + except arvados.errors.KeepRequestError: + # Something is wrong, cached manifest is not valid. + return False + return True def collection_file_paths(self, col, path_prefix='.'): """Return a list of file paths by recursively go through the entire collection `col`""" @@ -719,7 +987,7 @@ class ArvPutUploadJob(object): try: fcntl.flock(fileobj, fcntl.LOCK_EX | fcntl.LOCK_NB) except IOError: - raise ResumeCacheConflict("{} locked".format(fileobj.name)) + raise ResumeCacheConflict(u"{} locked".format(fileobj.name)) def _save_state(self): """ @@ -732,6 +1000,7 @@ class ArvPutUploadJob(object): state = json.dumps(self._state) try: new_cache = tempfile.NamedTemporaryFile( + mode='w+', dir=os.path.dirname(self._cache_filename), delete=False) self._lock_file(new_cache) new_cache.write(state) @@ -751,6 +1020,9 @@ class ArvPutUploadJob(object): def collection_name(self): return self._my_collection().api_response()['name'] if self._my_collection().api_response() else None + def collection_trash_at(self): + return self._my_collection().get_trash_at() + def manifest_locator(self): return self._my_collection().manifest_locator() @@ -759,7 +1031,7 @@ class ArvPutUploadJob(object): m = self._my_collection().stripped_manifest().encode() local_pdh = '{}+{}'.format(hashlib.md5(m).hexdigest(), len(m)) if pdh != local_pdh: - logger.warning("\n".join([ + self.logger.warning("\n".join([ "arv-put: API server provided PDH differs from local manifest.", " This should not happen; showing API server version."])) return pdh @@ -797,23 +1069,24 @@ class ArvPutUploadJob(object): datablocks = self._datablocks_on_item(self._my_collection()) return datablocks - -def expected_bytes_for(pathlist): - # Walk the given directory trees and stat files, adding up file sizes, - # so we can display progress as percent - bytesum = 0 - for path in pathlist: - if os.path.isdir(path): - for filename in arvados.util.listdir_recursive(path): - bytesum += os.path.getsize(os.path.join(path, filename)) - elif not os.path.isfile(path): - return None - else: - bytesum += os.path.getsize(path) - return bytesum - _machine_format = "{} {}: {{}} written {{}} total\n".format(sys.argv[0], os.getpid()) + +# Simulate glob.glob() matching behavior without the need to scan the filesystem +# Note: fnmatch() doesn't work correctly when used with pathnames. For example the +# pattern 'tests/*.py' will match 'tests/run_test.py' and also 'tests/subdir/run_test.py', +# so instead we're using it on every path component. +def pathname_match(pathname, pattern): + name = pathname.split(os.sep) + # Fix patterns like 'some/subdir/' or 'some//subdir' + pat = [x for x in pattern.split(os.sep) if x != '' and x != '.'] + if len(name) != len(pat): + return False + for i in range(len(name)): + if not fnmatch.fnmatch(name[i], pat[i]): + return False + return True + def machine_progress(bytes_written, bytes_expected): return _machine_format.format( bytes_written, -1 if (bytes_expected is None) else bytes_expected) @@ -831,9 +1104,6 @@ def progress_writer(progress_func, outfile=sys.stderr): outfile.write(progress_func(bytes_written, bytes_expected)) return write_progress -def exit_signal_handler(sigcode, frame): - sys.exit(-sigcode) - def desired_project_uuid(api_client, project_uuid, num_retries): if not project_uuid: query = api_client.users().current() @@ -845,15 +1115,66 @@ def desired_project_uuid(api_client, project_uuid, num_retries): raise ValueError("Not a valid project UUID: {}".format(project_uuid)) return query.execute(num_retries=num_retries)['uuid'] -def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): +def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr, + install_sig_handlers=True): global api_client - logger = logging.getLogger('arvados.arv_put') - logger.setLevel(logging.INFO) args = parse_arguments(arguments) + logger = logging.getLogger('arvados.arv_put') + if args.silent: + logger.setLevel(logging.WARNING) + else: + logger.setLevel(logging.INFO) status = 0 + + request_id = arvados.util.new_request_id() + + formatter = ArvPutLogFormatter(request_id) + logging.getLogger('arvados').handlers[0].setFormatter(formatter) + if api_client is None: - api_client = arvados.api('v1') + api_client = arvados.api('v1', request_id=request_id) + + if install_sig_handlers: + arv_cmd.install_signal_handlers() + + # Trash arguments validation + trash_at = None + if args.trash_at is not None: + # ciso8601 considers YYYYMM as invalid but YYYY-MM as valid, so here we + # make sure the user provides a complete YYYY-MM-DD date. + if not re.match(r'^\d{4}(?P-?)\d{2}?(?P=dash)\d{2}', args.trash_at): + logger.error("--trash-at argument format invalid, use --help to see examples.") + sys.exit(1) + # Check if no time information was provided. In that case, assume end-of-day. + if re.match(r'^\d{4}(?P-?)\d{2}?(?P=dash)\d{2}$', args.trash_at): + args.trash_at += 'T23:59:59' + try: + trash_at = ciso8601.parse_datetime(args.trash_at) + except: + logger.error("--trash-at argument format invalid, use --help to see examples.") + sys.exit(1) + else: + if trash_at.tzinfo is not None: + # Timezone aware datetime provided. + utcoffset = -trash_at.utcoffset() + else: + # Timezone naive datetime provided. Assume is local. + if time.daylight: + utcoffset = datetime.timedelta(seconds=time.altzone) + else: + utcoffset = datetime.timedelta(seconds=time.timezone) + # Convert to UTC timezone naive datetime. + trash_at = trash_at.replace(tzinfo=None) + utcoffset + + if trash_at <= datetime.datetime.utcnow(): + logger.error("--trash-at argument must be set in the future") + sys.exit(1) + if args.trash_after is not None: + if args.trash_after < 1: + logger.error("--trash-after argument must be >= 1") + sys.exit(1) + trash_at = datetime.timedelta(seconds=(args.trash_after * 24 * 60 * 60)) # Determine the name to use if args.name: @@ -889,19 +1210,62 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): else: reporter = None + # Split storage-classes argument + storage_classes = None + if args.storage_classes: + storage_classes = args.storage_classes.strip().replace(' ', '').split(',') + + # Setup exclude regex from all the --exclude arguments provided + name_patterns = [] + exclude_paths = [] + exclude_names = None + if len(args.exclude) > 0: + # We're supporting 2 kinds of exclusion patterns: + # 1) --exclude '*.jpg' (file/dir name patterns, will only match + # the name, wherever the file is on the tree) + # 2.1) --exclude 'foo/bar' (file/dir path patterns, will match the + # entire path, and should be relative to + # any input dir argument) + # 2.2) --exclude './*.jpg' (Special case for excluding files/dirs + # placed directly underneath the input dir) + for p in args.exclude: + # Only relative paths patterns allowed + if p.startswith(os.sep): + logger.error("Cannot use absolute paths with --exclude") + sys.exit(1) + if os.path.dirname(p): + # We don't support of path patterns with '..' + p_parts = p.split(os.sep) + if '..' in p_parts: + logger.error( + "Cannot use path patterns that include or '..'") + sys.exit(1) + # Path search pattern + exclude_paths.append(p) + else: + # Name-only search pattern + name_patterns.append(p) + # For name only matching, we can combine all patterns into a single + # regexp, for better performance. + exclude_names = re.compile('|'.join( + [fnmatch.translate(p) for p in name_patterns] + )) if len(name_patterns) > 0 else None + # Show the user the patterns to be used, just in case they weren't + # specified inside quotes and got changed by the shell expansion. + logger.info("Exclude patterns: {}".format(args.exclude)) + # If this is used by a human, and there's at least one directory to be # uploaded, the expected bytes calculation can take a moment. if args.progress and any([os.path.isdir(f) for f in args.paths]): logger.info("Calculating upload size, this could take some time...") - bytes_expected = expected_bytes_for(args.paths) - try: writer = ArvPutUploadJob(paths = args.paths, resume = args.resume, use_cache = args.use_cache, + batch_mode= args.batch, filename = args.filename, reporter = reporter, - bytes_expected = bytes_expected, + api_client = api_client, num_retries = args.retries, replication_desired = args.replication, put_threads = args.threads, @@ -909,14 +1273,28 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): owner_uuid = project_uuid, ensure_unique_name = True, update_collection = args.update_collection, + storage_classes=storage_classes, logger=logger, - dry_run=args.dry_run) + dry_run=args.dry_run, + follow_links=args.follow_links, + exclude_paths=exclude_paths, + exclude_names=exclude_names, + trash_at=trash_at) except ResumeCacheConflict: logger.error("\n".join([ "arv-put: Another process is already uploading this data.", " Use --no-cache if this is really what you want."])) sys.exit(1) - except CollectionUpdateError as error: + except ResumeCacheInvalidError: + logger.error("\n".join([ + "arv-put: Resume cache contains invalid signature: it may have expired", + " or been created with another Arvados user's credentials.", + " Switch user or use one of the following options to restart upload:", + " --no-resume to start a new resume cache.", + " --no-cache to disable resume cache.", + " --batch to ignore the resume cache if invalid."])) + sys.exit(1) + except (CollectionUpdateError, PathDoesNotExistError) as error: logger.error("\n".join([ "arv-put: %s" % str(error)])) sys.exit(1) @@ -927,11 +1305,6 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): # No files pending for upload sys.exit(0) - # Install our signal handler for each code in CAUGHT_SIGNALS, and save - # the originals. - orig_signal_handlers = {sigcode: signal.signal(sigcode, exit_signal_handler) - for sigcode in CAUGHT_SIGNALS} - if not args.dry_run and not args.update_collection and args.resume and writer.bytes_written > 0: logger.warning("\n".join([ "arv-put: Resuming previous upload from last checkpoint.", @@ -942,16 +1315,10 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): output = None try: writer.start(save_collection=not(args.stream or args.raw)) - except arvados.errors.ApiError as error: + except (arvados.errors.ApiError, arvados.errors.KeepWriteError) as error: logger.error("\n".join([ "arv-put: %s" % str(error)])) sys.exit(1) - except ArvPutUploadIsPending: - # Dry run check successful, return proper exit code. - sys.exit(2) - except ArvPutUploadNotPending: - # No files pending for upload - sys.exit(0) if args.progress: # Print newline to split stderr from stdout for humans. logger.info("\n") @@ -963,12 +1330,23 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): output = writer.manifest_text() elif args.raw: output = ','.join(writer.data_locators()) - else: + elif writer.manifest_locator() is not None: try: + expiration_notice = "" + if writer.collection_trash_at() is not None: + # Get the local timezone-naive version, and log it with timezone information. + if time.daylight: + local_trash_at = writer.collection_trash_at().replace(tzinfo=None) - datetime.timedelta(seconds=time.altzone) + else: + local_trash_at = writer.collection_trash_at().replace(tzinfo=None) - datetime.timedelta(seconds=time.timezone) + expiration_notice = ". It will expire on {} {}.".format( + local_trash_at.strftime("%Y-%m-%d %H:%M:%S"), time.strftime("%z")) if args.update_collection: - logger.info("Collection updated: '{}'".format(writer.collection_name())) + logger.info(u"Collection updated: '{}'{}".format( + writer.collection_name(), expiration_notice)) else: - logger.info("Collection saved as '{}'".format(writer.collection_name())) + logger.info(u"Collection saved as '{}'{}".format( + writer.collection_name(), expiration_notice)) if args.portable_data_hash: output = writer.portable_data_hash() else: @@ -978,17 +1356,19 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): "arv-put: Error creating Collection on project: {}.".format( error)) status = 1 + else: + status = 1 # Print the locator (uuid) of the new collection. if output is None: status = status or 1 - else: + elif not args.silent: stdout.write(output) if not output.endswith('\n'): stdout.write('\n') - for sigcode, orig_handler in listitems(orig_signal_handlers): - signal.signal(sigcode, orig_handler) + if install_sig_handlers: + arv_cmd.restore_signal_handlers() if status != 0: sys.exit(status)