1 # Copyright (C) The Arvados Authors. All rights reserved.
3 # SPDX-License-Identifier: Apache-2.0
5 from __future__ import division
6 from future.utils import listitems, listvalues
7 from builtins import str
8 from builtins import object
11 import arvados.collection
32 from apiclient import errors as apiclient_errors
33 from arvados._version import __version__
34 from arvados.util import keep_locator_pattern
36 import arvados.commands._util as arv_cmd
40 upload_opts = argparse.ArgumentParser(add_help=False)
42 upload_opts.add_argument('--version', action='version',
43 version="%s %s" % (sys.argv[0], __version__),
44 help='Print version and exit.')
45 upload_opts.add_argument('paths', metavar='path', type=str, nargs='*',
47 Local file or directory. If path is a directory reference with a trailing
48 slash, then just upload the directory's contents; otherwise upload the
49 directory itself. Default: read from standard input.
52 _group = upload_opts.add_mutually_exclusive_group()
54 _group.add_argument('--max-manifest-depth', type=int, metavar='N',
55 default=-1, help=argparse.SUPPRESS)
57 _group.add_argument('--normalize', action='store_true',
59 Normalize the manifest by re-ordering files and streams after writing
63 _group.add_argument('--dry-run', action='store_true', default=False,
65 Don't actually upload files, but only check if any file should be
66 uploaded. Exit with code=2 when files are pending for upload.
69 _group = upload_opts.add_mutually_exclusive_group()
71 _group.add_argument('--as-stream', action='store_true', dest='stream',
76 _group.add_argument('--stream', action='store_true',
78 Store the file content and display the resulting manifest on
79 stdout. Do not write the manifest to Keep or save a Collection object
83 _group.add_argument('--as-manifest', action='store_true', dest='manifest',
85 Synonym for --manifest.
88 _group.add_argument('--in-manifest', action='store_true', dest='manifest',
90 Synonym for --manifest.
93 _group.add_argument('--manifest', action='store_true',
95 Store the file data and resulting manifest in Keep, save a Collection
96 object in Arvados, and display the manifest locator (Collection uuid)
97 on stdout. This is the default behavior.
100 _group.add_argument('--as-raw', action='store_true', dest='raw',
105 _group.add_argument('--raw', action='store_true',
107 Store the file content and display the data block locators on stdout,
108 separated by commas, with a trailing newline. Do not store a
112 upload_opts.add_argument('--update-collection', type=str, default=None,
113 dest='update_collection', metavar="UUID", help="""
114 Update an existing collection identified by the given Arvados collection
115 UUID. All new local files will be uploaded.
118 upload_opts.add_argument('--use-filename', type=str, default=None,
119 dest='filename', help="""
120 Synonym for --filename.
123 upload_opts.add_argument('--filename', type=str, default=None,
125 Use the given filename in the manifest, instead of the name of the
126 local file. This is useful when "-" or "/dev/stdin" is given as an
127 input file. It can be used only if there is exactly one path given and
128 it is not a directory. Implies --manifest.
131 upload_opts.add_argument('--portable-data-hash', action='store_true',
133 Print the portable data hash instead of the Arvados UUID for the collection
134 created by the upload.
137 upload_opts.add_argument('--replication', type=int, metavar='N', default=None,
139 Set the replication level for the new collection: how many different
140 physical storage devices (e.g., disks) should have a copy of each data
141 block. Default is to use the server-provided default (if any) or 2.
144 upload_opts.add_argument('--storage-classes', help="""
145 Specify comma separated list of storage classes to be used when saving data to Keep.
148 upload_opts.add_argument('--threads', type=int, metavar='N', default=None,
150 Set the number of upload threads to be used. Take into account that
151 using lots of threads will increase the RAM requirements. Default is
153 On high latency installations, using a greater number will improve
157 run_opts = argparse.ArgumentParser(add_help=False)
159 run_opts.add_argument('--project-uuid', metavar='UUID', help="""
160 Store the collection in the specified project, instead of your Home
164 run_opts.add_argument('--name', help="""
165 Save the collection with the specified name.
168 run_opts.add_argument('--exclude', metavar='PATTERN', default=[],
169 action='append', help="""
170 Exclude files and directories whose names match the given glob pattern. When
171 using a path-like pattern like 'subdir/*.txt', all text files inside 'subdir'
172 directory, relative to the provided input dirs will be excluded.
173 When using a filename pattern like '*.txt', any text file will be excluded
174 no matter where is placed.
175 For the special case of needing to exclude only files or dirs directly below
176 the given input directory, you can use a pattern like './exclude_this.gif'.
177 You can specify multiple patterns by using this argument more than once.
180 _group = run_opts.add_mutually_exclusive_group()
181 _group.add_argument('--progress', action='store_true',
183 Display human-readable progress on stderr (bytes and, if possible,
184 percentage of total data size). This is the default behavior when
188 _group.add_argument('--no-progress', action='store_true',
190 Do not display human-readable progress on stderr, even if stderr is a
194 _group.add_argument('--batch-progress', action='store_true',
196 Display machine-readable progress on stderr (bytes and, if known,
200 run_opts.add_argument('--silent', action='store_true',
202 Do not print any debug messages to console. (Any error messages will
206 _group = run_opts.add_mutually_exclusive_group()
207 _group.add_argument('--resume', action='store_true', default=True,
209 Continue interrupted uploads from cached state (default).
211 _group.add_argument('--no-resume', action='store_false', dest='resume',
213 Do not continue interrupted uploads from cached state.
216 _group = run_opts.add_mutually_exclusive_group()
217 _group.add_argument('--follow-links', action='store_true', default=True,
218 dest='follow_links', help="""
219 Follow file and directory symlinks (default).
221 _group.add_argument('--no-follow-links', action='store_false', dest='follow_links',
223 Do not follow file and directory symlinks.
226 _group = run_opts.add_mutually_exclusive_group()
227 _group.add_argument('--cache', action='store_true', dest='use_cache', default=True,
229 Save upload state in a cache file for resuming (default).
231 _group.add_argument('--no-cache', action='store_false', dest='use_cache',
233 Do not save upload state in a cache file for resuming.
236 arg_parser = argparse.ArgumentParser(
237 description='Copy data from the local filesystem to Keep.',
238 parents=[upload_opts, run_opts, arv_cmd.retry_opt])
240 def parse_arguments(arguments):
241 args = arg_parser.parse_args(arguments)
243 if len(args.paths) == 0:
246 args.paths = ["-" if x == "/dev/stdin" else x for x in args.paths]
248 if len(args.paths) != 1 or os.path.isdir(args.paths[0]):
251 --filename argument cannot be used when storing a directory or
255 # Turn on --progress by default if stderr is a tty.
256 if (not (args.batch_progress or args.no_progress or args.silent)
257 and os.isatty(sys.stderr.fileno())):
260 # Turn off --resume (default) if --no-cache is used.
261 if not args.use_cache:
264 if args.paths == ['-']:
265 if args.update_collection:
267 --update-collection cannot be used when reading from stdin.
270 args.use_cache = False
271 if not args.filename:
272 args.filename = 'stdin'
274 # Remove possible duplicated patterns
275 if len(args.exclude) > 0:
276 args.exclude = list(set(args.exclude))
281 class PathDoesNotExistError(Exception):
285 class CollectionUpdateError(Exception):
289 class ResumeCacheConflict(Exception):
293 class ResumeCacheInvalidError(Exception):
296 class ArvPutArgumentConflict(Exception):
300 class ArvPutUploadIsPending(Exception):
304 class ArvPutUploadNotPending(Exception):
308 class FileUploadList(list):
309 def __init__(self, dry_run=False):
311 self.dry_run = dry_run
313 def append(self, other):
315 raise ArvPutUploadIsPending()
316 super(FileUploadList, self).append(other)
319 # Appends the X-Request-Id to the log message when log level is ERROR or DEBUG
320 class ArvPutLogFormatter(logging.Formatter):
321 std_fmtr = logging.Formatter(arvados.log_format, arvados.log_date_format)
323 request_id_informed = False
325 def __init__(self, request_id):
326 self.err_fmtr = logging.Formatter(
327 arvados.log_format+' (X-Request-Id: {})'.format(request_id),
328 arvados.log_date_format)
330 def format(self, record):
331 if (not self.request_id_informed) and (record.levelno in (logging.DEBUG, logging.ERROR)):
332 self.request_id_informed = True
333 return self.err_fmtr.format(record)
334 return self.std_fmtr.format(record)
337 class ResumeCache(object):
338 CACHE_DIR = '.cache/arvados/arv-put'
340 def __init__(self, file_spec):
341 self.cache_file = open(file_spec, 'a+')
342 self._lock_file(self.cache_file)
343 self.filename = self.cache_file.name
346 def make_path(cls, args):
348 md5.update(arvados.config.get('ARVADOS_API_HOST', '!nohost').encode())
349 realpaths = sorted(os.path.realpath(path) for path in args.paths)
350 md5.update(b'\0'.join([p.encode() for p in realpaths]))
351 if any(os.path.isdir(path) for path in realpaths):
354 md5.update(args.filename.encode())
356 arv_cmd.make_home_conf_dir(cls.CACHE_DIR, 0o700, 'raise'),
359 def _lock_file(self, fileobj):
361 fcntl.flock(fileobj, fcntl.LOCK_EX | fcntl.LOCK_NB)
363 raise ResumeCacheConflict("{} locked".format(fileobj.name))
366 self.cache_file.seek(0)
367 return json.load(self.cache_file)
369 def check_cache(self, api_client=None, num_retries=0):
374 if "_finished_streams" in state and len(state["_finished_streams"]) > 0:
375 locator = state["_finished_streams"][0][1][0]
376 elif "_current_stream_locators" in state and len(state["_current_stream_locators"]) > 0:
377 locator = state["_current_stream_locators"][0]
378 if locator is not None:
379 kc = arvados.keep.KeepClient(api_client=api_client)
380 kc.head(locator, num_retries=num_retries)
381 except Exception as e:
386 def save(self, data):
388 new_cache_fd, new_cache_name = tempfile.mkstemp(
389 dir=os.path.dirname(self.filename))
390 self._lock_file(new_cache_fd)
391 new_cache = os.fdopen(new_cache_fd, 'r+')
392 json.dump(data, new_cache)
393 os.rename(new_cache_name, self.filename)
394 except (IOError, OSError, ResumeCacheConflict):
396 os.unlink(new_cache_name)
397 except NameError: # mkstemp failed.
400 self.cache_file.close()
401 self.cache_file = new_cache
404 self.cache_file.close()
408 os.unlink(self.filename)
409 except OSError as error:
410 if error.errno != errno.ENOENT: # That's what we wanted anyway.
416 self.__init__(self.filename)
419 class ArvPutUploadJob(object):
420 CACHE_DIR = '.cache/arvados/arv-put'
422 'manifest' : None, # Last saved manifest checkpoint
423 'files' : {} # Previous run file list: {path : {size, mtime}}
426 def __init__(self, paths, resume=True, use_cache=True, reporter=None,
427 name=None, owner_uuid=None, api_client=None,
428 ensure_unique_name=False, num_retries=None,
429 put_threads=None, replication_desired=None, filename=None,
430 update_time=60.0, update_collection=None, storage_classes=None,
431 logger=logging.getLogger('arvados.arv_put'), dry_run=False,
432 follow_links=True, exclude_paths=[], exclude_names=None):
435 self.use_cache = use_cache
437 self.reporter = reporter
438 # This will set to 0 before start counting, if no special files are going
440 self.bytes_expected = None
441 self.bytes_written = 0
442 self.bytes_skipped = 0
444 self.owner_uuid = owner_uuid
445 self.ensure_unique_name = ensure_unique_name
446 self.num_retries = num_retries
447 self.replication_desired = replication_desired
448 self.put_threads = put_threads
449 self.filename = filename
450 self.storage_classes = storage_classes
451 self._api_client = api_client
452 self._state_lock = threading.Lock()
453 self._state = None # Previous run state (file list & manifest)
454 self._current_files = [] # Current run file list
455 self._cache_file = None
456 self._collection_lock = threading.Lock()
457 self._remote_collection = None # Collection being updated (if asked)
458 self._local_collection = None # Collection from previous run manifest
459 self._file_paths = set() # Files to be updated in remote collection
460 self._stop_checkpointer = threading.Event()
461 self._checkpointer = threading.Thread(target=self._update_task)
462 self._checkpointer.daemon = True
463 self._update_task_time = update_time # How many seconds wait between update runs
464 self._files_to_upload = FileUploadList(dry_run=dry_run)
465 self._upload_started = False
467 self.dry_run = dry_run
468 self._checkpoint_before_quit = True
469 self.follow_links = follow_links
470 self.exclude_paths = exclude_paths
471 self.exclude_names = exclude_names
473 if not self.use_cache and self.resume:
474 raise ArvPutArgumentConflict('resume cannot be True when use_cache is False')
476 # Check for obvious dry-run responses
477 if self.dry_run and (not self.use_cache or not self.resume):
478 raise ArvPutUploadIsPending()
480 # Load cached data if any and if needed
481 self._setup_state(update_collection)
483 # Build the upload file list, excluding requested files and counting the
484 # bytes expected to be uploaded.
485 self._build_upload_list()
487 def _build_upload_list(self):
489 Scan the requested paths to count file sizes, excluding requested files
490 and dirs and building the upload file list.
492 # If there aren't special files to be read, reset total bytes count to zero
494 if not any([p for p in self.paths
495 if not (os.path.isfile(p) or os.path.isdir(p))]):
496 self.bytes_expected = 0
498 for path in self.paths:
499 # Test for stdin first, in case some file named '-' exist
502 raise ArvPutUploadIsPending()
503 self._write_stdin(self.filename or 'stdin')
504 elif not os.path.exists(path):
505 raise PathDoesNotExistError("file or directory '{}' does not exist.".format(path))
506 elif os.path.isdir(path):
507 # Use absolute paths on cache index so CWD doesn't interfere
508 # with the caching logic.
510 path = os.path.abspath(path)
511 if orig_path[-1:] == os.sep:
512 # When passing a directory reference with a trailing slash,
513 # its contents should be uploaded directly to the
517 # When passing a directory reference with no trailing slash,
518 # upload the directory to the collection's root.
519 prefixdir = os.path.dirname(path)
521 for root, dirs, files in os.walk(path,
522 followlinks=self.follow_links):
523 root_relpath = os.path.relpath(root, path)
524 if root_relpath == '.':
526 # Exclude files/dirs by full path matching pattern
527 if self.exclude_paths:
528 dirs[:] = [d for d in dirs
529 if not any(pathname_match(
530 os.path.join(root_relpath, d), pat)
531 for pat in self.exclude_paths)]
532 files = [f for f in files
533 if not any(pathname_match(
534 os.path.join(root_relpath, f), pat)
535 for pat in self.exclude_paths)]
536 # Exclude files/dirs by name matching pattern
537 if self.exclude_names is not None:
538 dirs[:] = [d for d in dirs
539 if not self.exclude_names.match(d)]
540 files = [f for f in files
541 if not self.exclude_names.match(f)]
542 # Make os.walk()'s dir traversing order deterministic
546 filepath = os.path.join(root, f)
547 # Add its size to the total bytes count (if applicable)
548 if self.follow_links or (not os.path.islink(filepath)):
549 if self.bytes_expected is not None:
550 self.bytes_expected += os.path.getsize(filepath)
551 self._check_file(filepath,
552 os.path.join(root[len(prefixdir):], f))
554 filepath = os.path.abspath(path)
555 # Add its size to the total bytes count (if applicable)
556 if self.follow_links or (not os.path.islink(filepath)):
557 if self.bytes_expected is not None:
558 self.bytes_expected += os.path.getsize(filepath)
559 self._check_file(filepath,
560 self.filename or os.path.basename(path))
561 # If dry-mode is on, and got up to this point, then we should notify that
562 # there aren't any file to upload.
564 raise ArvPutUploadNotPending()
565 # Remove local_collection's files that don't exist locally anymore, so the
566 # bytes_written count is correct.
567 for f in self.collection_file_paths(self._local_collection,
569 if f != 'stdin' and f != self.filename and not f in self._file_paths:
570 self._local_collection.remove(f)
572 def start(self, save_collection):
574 Start supporting thread & file uploading
576 self._checkpointer.start()
578 # Update bytes_written from current local collection and
579 # report initial progress.
582 self._upload_started = True # Used by the update thread to start checkpointing
584 except (SystemExit, Exception) as e:
585 self._checkpoint_before_quit = False
586 # Log stack trace only when Ctrl-C isn't pressed (SIGINT)
587 # Note: We're expecting SystemExit instead of
588 # KeyboardInterrupt because we have a custom signal
589 # handler in place that raises SystemExit with the catched
591 if isinstance(e, PathDoesNotExistError):
592 # We aren't interested in the traceback for this case
594 elif not isinstance(e, SystemExit) or e.code != -2:
595 self.logger.warning("Abnormal termination:\n{}".format(
596 traceback.format_exc()))
600 # Stop the thread before doing anything else
601 self._stop_checkpointer.set()
602 self._checkpointer.join()
603 if self._checkpoint_before_quit:
604 # Commit all pending blocks & one last _update()
605 self._local_collection.manifest_text()
606 self._update(final=True)
608 self.save_collection()
610 self._cache_file.close()
612 def save_collection(self):
614 # Check if files should be updated on the remote collection.
615 for fp in self._file_paths:
616 remote_file = self._remote_collection.find(fp)
618 # File don't exist on remote collection, copy it.
619 self._remote_collection.copy(fp, fp, self._local_collection)
620 elif remote_file != self._local_collection.find(fp):
621 # A different file exist on remote collection, overwrite it.
622 self._remote_collection.copy(fp, fp, self._local_collection, overwrite=True)
624 # The file already exist on remote collection, skip it.
626 self._remote_collection.save(storage_classes=self.storage_classes,
627 num_retries=self.num_retries)
629 if self.storage_classes is None:
630 self.storage_classes = ['default']
631 self._local_collection.save_new(
632 name=self.name, owner_uuid=self.owner_uuid,
633 storage_classes=self.storage_classes,
634 ensure_unique_name=self.ensure_unique_name,
635 num_retries=self.num_retries)
637 def destroy_cache(self):
640 os.unlink(self._cache_filename)
641 except OSError as error:
642 # That's what we wanted anyway.
643 if error.errno != errno.ENOENT:
645 self._cache_file.close()
647 def _collection_size(self, collection):
649 Recursively get the total size of the collection
652 for item in listvalues(collection):
653 if isinstance(item, arvados.collection.Collection) or isinstance(item, arvados.collection.Subcollection):
654 size += self._collection_size(item)
659 def _update_task(self):
661 Periodically called support task. File uploading is
662 asynchronous so we poll status from the collection.
664 while not self._stop_checkpointer.wait(1 if not self._upload_started else self._update_task_time):
667 def _update(self, final=False):
669 Update cached manifest text and report progress.
671 if self._upload_started:
672 with self._collection_lock:
673 self.bytes_written = self._collection_size(self._local_collection)
676 manifest = self._local_collection.manifest_text()
678 # Get the manifest text without comitting pending blocks
679 manifest = self._local_collection.manifest_text(strip=False,
683 with self._state_lock:
684 self._state['manifest'] = manifest
688 except Exception as e:
689 self.logger.error("Unexpected error trying to save cache file: {}".format(e))
691 self.bytes_written = self.bytes_skipped
692 # Call the reporter, if any
693 self.report_progress()
695 def report_progress(self):
696 if self.reporter is not None:
697 self.reporter(self.bytes_written, self.bytes_expected)
699 def _write_stdin(self, filename):
700 output = self._local_collection.open(filename, 'wb')
701 self._write(sys.stdin, output)
704 def _check_file(self, source, filename):
706 Check if this file needs to be uploaded
708 # Ignore symlinks when requested
709 if (not self.follow_links) and os.path.islink(source):
712 should_upload = False
713 new_file_in_cache = False
714 # Record file path for updating the remote collection before exiting
715 self._file_paths.add(filename)
717 with self._state_lock:
718 # If no previous cached data on this file, store it for an eventual
720 if source not in self._state['files']:
721 self._state['files'][source] = {
722 'mtime': os.path.getmtime(source),
723 'size' : os.path.getsize(source)
725 new_file_in_cache = True
726 cached_file_data = self._state['files'][source]
728 # Check if file was already uploaded (at least partially)
729 file_in_local_collection = self._local_collection.find(filename)
731 # If not resuming, upload the full file.
734 # New file detected from last run, upload it.
735 elif new_file_in_cache:
737 # Local file didn't change from last run.
738 elif cached_file_data['mtime'] == os.path.getmtime(source) and cached_file_data['size'] == os.path.getsize(source):
739 if not file_in_local_collection:
740 # File not uploaded yet, upload it completely
742 elif cached_file_data['size'] == file_in_local_collection.size():
743 # File already there, skip it.
744 self.bytes_skipped += cached_file_data['size']
745 elif cached_file_data['size'] > file_in_local_collection.size():
746 # File partially uploaded, resume!
747 resume_offset = file_in_local_collection.size()
748 self.bytes_skipped += resume_offset
751 # Inconsistent cache, re-upload the file
753 self._local_collection.remove(filename)
754 self.logger.warning("Uploaded version of file '{}' is bigger than local version, will re-upload it from scratch.".format(source))
755 # Local file differs from cached data, re-upload it.
757 if file_in_local_collection:
758 self._local_collection.remove(filename)
763 self._files_to_upload.append((source, resume_offset, filename))
764 except ArvPutUploadIsPending:
765 # This could happen when running on dry-mode, close cache file to
766 # avoid locking issues.
767 self._cache_file.close()
770 def _upload_files(self):
771 for source, resume_offset, filename in self._files_to_upload:
772 with open(source, 'rb') as source_fd:
773 with self._state_lock:
774 self._state['files'][source]['mtime'] = os.path.getmtime(source)
775 self._state['files'][source]['size'] = os.path.getsize(source)
776 if resume_offset > 0:
777 # Start upload where we left off
778 output = self._local_collection.open(filename, 'ab')
779 source_fd.seek(resume_offset)
782 output = self._local_collection.open(filename, 'wb')
783 self._write(source_fd, output)
784 output.close(flush=False)
786 def _write(self, source_fd, output):
788 data = source_fd.read(arvados.config.KEEP_BLOCK_SIZE)
793 def _my_collection(self):
794 return self._remote_collection if self.update else self._local_collection
796 def _setup_state(self, update_collection):
798 Create a new cache file or load a previously existing one.
800 # Load an already existing collection for update
801 if update_collection and re.match(arvados.util.collection_uuid_pattern,
804 self._remote_collection = arvados.collection.Collection(
805 update_collection, api_client=self._api_client)
806 except arvados.errors.ApiError as error:
807 raise CollectionUpdateError("Cannot read collection {} ({})".format(update_collection, error))
810 elif update_collection:
811 # Collection locator provided, but unknown format
812 raise CollectionUpdateError("Collection locator unknown: '{}'".format(update_collection))
815 # Set up cache file name from input paths.
817 md5.update(arvados.config.get('ARVADOS_API_HOST', '!nohost').encode())
818 realpaths = sorted(os.path.realpath(path) for path in self.paths)
819 md5.update(b'\0'.join([p.encode() for p in realpaths]))
821 md5.update(self.filename.encode())
822 cache_filename = md5.hexdigest()
823 cache_filepath = os.path.join(
824 arv_cmd.make_home_conf_dir(self.CACHE_DIR, 0o700, 'raise'),
826 if self.resume and os.path.exists(cache_filepath):
827 self.logger.info("Resuming upload from cache file {}".format(cache_filepath))
828 self._cache_file = open(cache_filepath, 'a+')
830 # --no-resume means start with a empty cache file.
831 self.logger.info("Creating new cache file at {}".format(cache_filepath))
832 self._cache_file = open(cache_filepath, 'w+')
833 self._cache_filename = self._cache_file.name
834 self._lock_file(self._cache_file)
835 self._cache_file.seek(0)
837 with self._state_lock:
840 self._state = json.load(self._cache_file)
841 if not set(['manifest', 'files']).issubset(set(self._state.keys())):
842 # Cache at least partially incomplete, set up new cache
843 self._state = copy.deepcopy(self.EMPTY_STATE)
845 # Cache file empty, set up new cache
846 self._state = copy.deepcopy(self.EMPTY_STATE)
848 self.logger.info("No cache usage requested for this run.")
849 # No cache file, set empty state
850 self._state = copy.deepcopy(self.EMPTY_STATE)
851 if not self._cached_manifest_valid():
852 raise ResumeCacheInvalidError()
853 # Load the previous manifest so we can check if files were modified remotely.
854 self._local_collection = arvados.collection.Collection(
855 self._state['manifest'],
856 replication_desired=self.replication_desired,
857 put_threads=self.put_threads,
858 api_client=self._api_client)
860 def _cached_manifest_valid(self):
862 Validate first block's signature to check if cached manifest is usable.
863 Cached manifest could be invalid because:
864 * Block signature expiration
865 * Block signatures belonging to a different user
867 if self._state.get('manifest', None) is None:
868 # No cached manifest yet, all good.
870 m = keep_locator_pattern.search(self._state['manifest'])
872 # No blocks found, no invalid block signatures.
874 loc = self._state['manifest'][m.start():m.end()]
875 kc = arvados.KeepClient(api_client=self._api_client,
876 num_retries=self.num_retries)
879 except arvados.errors.KeepRequestError:
880 # Something is wrong, cached manifest is not valid.
884 def collection_file_paths(self, col, path_prefix='.'):
885 """Return a list of file paths by recursively go through the entire collection `col`"""
887 for name, item in listitems(col):
888 if isinstance(item, arvados.arvfile.ArvadosFile):
889 file_paths.append(os.path.join(path_prefix, name))
890 elif isinstance(item, arvados.collection.Subcollection):
891 new_prefix = os.path.join(path_prefix, name)
892 file_paths += self.collection_file_paths(item, path_prefix=new_prefix)
895 def _lock_file(self, fileobj):
897 fcntl.flock(fileobj, fcntl.LOCK_EX | fcntl.LOCK_NB)
899 raise ResumeCacheConflict("{} locked".format(fileobj.name))
901 def _save_state(self):
903 Atomically save current state into cache.
905 with self._state_lock:
906 # We're not using copy.deepcopy() here because it's a lot slower
907 # than json.dumps(), and we're already needing JSON format to be
909 state = json.dumps(self._state)
911 new_cache = tempfile.NamedTemporaryFile(
913 dir=os.path.dirname(self._cache_filename), delete=False)
914 self._lock_file(new_cache)
915 new_cache.write(state)
918 os.rename(new_cache.name, self._cache_filename)
919 except (IOError, OSError, ResumeCacheConflict) as error:
920 self.logger.error("There was a problem while saving the cache file: {}".format(error))
922 os.unlink(new_cache_name)
923 except NameError: # mkstemp failed.
926 self._cache_file.close()
927 self._cache_file = new_cache
929 def collection_name(self):
930 return self._my_collection().api_response()['name'] if self._my_collection().api_response() else None
932 def manifest_locator(self):
933 return self._my_collection().manifest_locator()
935 def portable_data_hash(self):
936 pdh = self._my_collection().portable_data_hash()
937 m = self._my_collection().stripped_manifest().encode()
938 local_pdh = '{}+{}'.format(hashlib.md5(m).hexdigest(), len(m))
940 self.logger.warning("\n".join([
941 "arv-put: API server provided PDH differs from local manifest.",
942 " This should not happen; showing API server version."]))
945 def manifest_text(self, stream_name=".", strip=False, normalize=False):
946 return self._my_collection().manifest_text(stream_name, strip, normalize)
948 def _datablocks_on_item(self, item):
950 Return a list of datablock locators, recursively navigating
951 through subcollections
953 if isinstance(item, arvados.arvfile.ArvadosFile):
956 return ["d41d8cd98f00b204e9800998ecf8427e+0"]
959 for segment in item.segments():
960 loc = segment.locator
963 elif isinstance(item, arvados.collection.Collection):
964 l = [self._datablocks_on_item(x) for x in listvalues(item)]
965 # Fast list flattener method taken from:
966 # http://stackoverflow.com/questions/952914/making-a-flat-list-out-of-list-of-lists-in-python
967 return [loc for sublist in l for loc in sublist]
971 def data_locators(self):
972 with self._collection_lock:
973 # Make sure all datablocks are flushed before getting the locators
974 self._my_collection().manifest_text()
975 datablocks = self._datablocks_on_item(self._my_collection())
978 _machine_format = "{} {}: {{}} written {{}} total\n".format(sys.argv[0],
981 # Simulate glob.glob() matching behavior without the need to scan the filesystem
982 # Note: fnmatch() doesn't work correctly when used with pathnames. For example the
983 # pattern 'tests/*.py' will match 'tests/run_test.py' and also 'tests/subdir/run_test.py',
984 # so instead we're using it on every path component.
985 def pathname_match(pathname, pattern):
986 name = pathname.split(os.sep)
987 # Fix patterns like 'some/subdir/' or 'some//subdir'
988 pat = [x for x in pattern.split(os.sep) if x != '' and x != '.']
989 if len(name) != len(pat):
991 for i in range(len(name)):
992 if not fnmatch.fnmatch(name[i], pat[i]):
996 def machine_progress(bytes_written, bytes_expected):
997 return _machine_format.format(
998 bytes_written, -1 if (bytes_expected is None) else bytes_expected)
1000 def human_progress(bytes_written, bytes_expected):
1002 return "\r{}M / {}M {:.1%} ".format(
1003 bytes_written >> 20, bytes_expected >> 20,
1004 float(bytes_written) / bytes_expected)
1006 return "\r{} ".format(bytes_written)
1008 def progress_writer(progress_func, outfile=sys.stderr):
1009 def write_progress(bytes_written, bytes_expected):
1010 outfile.write(progress_func(bytes_written, bytes_expected))
1011 return write_progress
1013 def desired_project_uuid(api_client, project_uuid, num_retries):
1014 if not project_uuid:
1015 query = api_client.users().current()
1016 elif arvados.util.user_uuid_pattern.match(project_uuid):
1017 query = api_client.users().get(uuid=project_uuid)
1018 elif arvados.util.group_uuid_pattern.match(project_uuid):
1019 query = api_client.groups().get(uuid=project_uuid)
1021 raise ValueError("Not a valid project UUID: {}".format(project_uuid))
1022 return query.execute(num_retries=num_retries)['uuid']
1024 def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr,
1025 install_sig_handlers=True):
1028 args = parse_arguments(arguments)
1029 logger = logging.getLogger('arvados.arv_put')
1031 logger.setLevel(logging.WARNING)
1033 logger.setLevel(logging.INFO)
1036 request_id = arvados.util.new_request_id()
1038 formatter = ArvPutLogFormatter(request_id)
1039 logging.getLogger('arvados').handlers[0].setFormatter(formatter)
1041 if api_client is None:
1042 api_client = arvados.api('v1', request_id=request_id)
1044 if install_sig_handlers:
1045 arv_cmd.install_signal_handlers()
1047 # Determine the name to use
1049 if args.stream or args.raw:
1050 logger.error("Cannot use --name with --stream or --raw")
1052 elif args.update_collection:
1053 logger.error("Cannot use --name with --update-collection")
1055 collection_name = args.name
1057 collection_name = "Saved at {} by {}@{}".format(
1058 datetime.datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S UTC"),
1059 pwd.getpwuid(os.getuid()).pw_name,
1060 socket.gethostname())
1062 if args.project_uuid and (args.stream or args.raw):
1063 logger.error("Cannot use --project-uuid with --stream or --raw")
1066 # Determine the parent project
1068 project_uuid = desired_project_uuid(api_client, args.project_uuid,
1070 except (apiclient_errors.Error, ValueError) as error:
1075 reporter = progress_writer(human_progress)
1076 elif args.batch_progress:
1077 reporter = progress_writer(machine_progress)
1081 # Split storage-classes argument
1082 storage_classes = None
1083 if args.storage_classes:
1084 storage_classes = args.storage_classes.strip().split(',')
1085 if len(storage_classes) > 1:
1086 logger.error("Multiple storage classes are not supported currently.")
1090 # Setup exclude regex from all the --exclude arguments provided
1093 exclude_names = None
1094 if len(args.exclude) > 0:
1095 # We're supporting 2 kinds of exclusion patterns:
1096 # 1) --exclude '*.jpg' (file/dir name patterns, will only match
1097 # the name, wherever the file is on the tree)
1098 # 2.1) --exclude 'foo/bar' (file/dir path patterns, will match the
1099 # entire path, and should be relative to
1100 # any input dir argument)
1101 # 2.2) --exclude './*.jpg' (Special case for excluding files/dirs
1102 # placed directly underneath the input dir)
1103 for p in args.exclude:
1104 # Only relative paths patterns allowed
1105 if p.startswith(os.sep):
1106 logger.error("Cannot use absolute paths with --exclude")
1108 if os.path.dirname(p):
1109 # We don't support of path patterns with '..'
1110 p_parts = p.split(os.sep)
1113 "Cannot use path patterns that include or '..'")
1115 # Path search pattern
1116 exclude_paths.append(p)
1118 # Name-only search pattern
1119 name_patterns.append(p)
1120 # For name only matching, we can combine all patterns into a single
1121 # regexp, for better performance.
1122 exclude_names = re.compile('|'.join(
1123 [fnmatch.translate(p) for p in name_patterns]
1124 )) if len(name_patterns) > 0 else None
1125 # Show the user the patterns to be used, just in case they weren't
1126 # specified inside quotes and got changed by the shell expansion.
1127 logger.info("Exclude patterns: {}".format(args.exclude))
1129 # If this is used by a human, and there's at least one directory to be
1130 # uploaded, the expected bytes calculation can take a moment.
1131 if args.progress and any([os.path.isdir(f) for f in args.paths]):
1132 logger.info("Calculating upload size, this could take some time...")
1134 writer = ArvPutUploadJob(paths = args.paths,
1135 resume = args.resume,
1136 use_cache = args.use_cache,
1137 filename = args.filename,
1138 reporter = reporter,
1139 api_client = api_client,
1140 num_retries = args.retries,
1141 replication_desired = args.replication,
1142 put_threads = args.threads,
1143 name = collection_name,
1144 owner_uuid = project_uuid,
1145 ensure_unique_name = True,
1146 update_collection = args.update_collection,
1147 storage_classes=storage_classes,
1149 dry_run=args.dry_run,
1150 follow_links=args.follow_links,
1151 exclude_paths=exclude_paths,
1152 exclude_names=exclude_names)
1153 except ResumeCacheConflict:
1154 logger.error("\n".join([
1155 "arv-put: Another process is already uploading this data.",
1156 " Use --no-cache if this is really what you want."]))
1158 except ResumeCacheInvalidError:
1159 logger.error("\n".join([
1160 "arv-put: Cache seems to contain invalid data: it may have expired",
1161 " or been created with another arvados user's credentials.",
1162 " Use --no-resume to start a new cache file.",
1163 " Use --no-cache to skip current cache file usage."]))
1165 except CollectionUpdateError as error:
1166 logger.error("\n".join([
1167 "arv-put: %s" % str(error)]))
1169 except ArvPutUploadIsPending:
1170 # Dry run check successful, return proper exit code.
1172 except ArvPutUploadNotPending:
1173 # No files pending for upload
1175 except PathDoesNotExistError as error:
1176 logger.error("\n".join([
1177 "arv-put: %s" % str(error)]))
1180 if not args.dry_run and not args.update_collection and args.resume and writer.bytes_written > 0:
1181 logger.warning("\n".join([
1182 "arv-put: Resuming previous upload from last checkpoint.",
1183 " Use the --no-resume option to start over."]))
1185 if not args.dry_run:
1186 writer.report_progress()
1189 writer.start(save_collection=not(args.stream or args.raw))
1190 except arvados.errors.ApiError as error:
1191 logger.error("\n".join([
1192 "arv-put: %s" % str(error)]))
1195 if args.progress: # Print newline to split stderr from stdout for humans.
1200 output = writer.manifest_text(normalize=True)
1202 output = writer.manifest_text()
1204 output = ','.join(writer.data_locators())
1207 if args.update_collection:
1208 logger.info("Collection updated: '{}'".format(writer.collection_name()))
1210 logger.info("Collection saved as '{}'".format(writer.collection_name()))
1211 if args.portable_data_hash:
1212 output = writer.portable_data_hash()
1214 output = writer.manifest_locator()
1215 except apiclient_errors.Error as error:
1217 "arv-put: Error creating Collection on project: {}.".format(
1221 # Print the locator (uuid) of the new collection.
1223 status = status or 1
1224 elif not args.silent:
1225 stdout.write(output)
1226 if not output.endswith('\n'):
1229 if install_sig_handlers:
1230 arv_cmd.restore_signal_handlers()
1239 if __name__ == '__main__':