X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1c96d4eb740dc4285d9f30ba0ce73499f7b7d59e..3860042ac5783cddd368d8997991b0d1f8e9a111:/sdk/python/arvados/commands/put.py diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py index 88956cdce6..5b46ba75b7 100644 --- a/sdk/python/arvados/commands/put.py +++ b/sdk/python/arvados/commands/put.py @@ -24,6 +24,7 @@ import tempfile import threading import time from apiclient import errors as apiclient_errors +from arvados._version import __version__ import arvados.commands._util as arv_cmd @@ -32,6 +33,9 @@ api_client = None upload_opts = argparse.ArgumentParser(add_help=False) +upload_opts.add_argument('--version', action='version', + version="%s %s" % (sys.argv[0], __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. @@ -48,6 +52,12 @@ Normalize the manifest by re-ordering files and streams after writing data. """) +_group.add_argument('--dry-run', action='store_true', default=False, + help=""" +Don't actually upload files, but only check if any file should be +uploaded. Exit with code=2 when files are pending for upload. +""") + _group = upload_opts.add_mutually_exclusive_group() _group.add_argument('--as-stream', action='store_true', dest='stream', @@ -123,6 +133,15 @@ 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('--threads', type=int, metavar='N', default=None, + help=""" +Set the number of upload threads to be used. Take into account that +using lots of threads will increase the RAM requirements. Default is +to use 2 threads. +On high latency installations, using a greater number will improve +overall throughput. +""") + run_opts = argparse.ArgumentParser(add_help=False) run_opts.add_argument('--project-uuid', metavar='UUID', help=""" @@ -222,9 +241,30 @@ class CollectionUpdateError(Exception): class ResumeCacheConflict(Exception): pass + class ArvPutArgumentConflict(Exception): pass + +class ArvPutUploadIsPending(Exception): + pass + + +class ArvPutUploadNotPending(Exception): + pass + + +class FileUploadList(list): + def __init__(self, dry_run=False): + list.__init__(self) + self.dry_run = dry_run + + def append(self, other): + if self.dry_run: + raise ArvPutUploadIsPending() + super(FileUploadList, self).append(other) + + class ResumeCache(object): CACHE_DIR = '.cache/arvados/arv-put' @@ -316,8 +356,10 @@ class ArvPutUploadJob(object): def __init__(self, paths, resume=True, use_cache=True, reporter=None, bytes_expected=None, name=None, owner_uuid=None, - ensure_unique_name=False, num_retries=None, replication_desired=None, - filename=None, update_time=20.0, update_collection=None): + 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): self.paths = paths self.resume = resume self.use_cache = use_cache @@ -331,6 +373,7 @@ class ArvPutUploadJob(object): self.ensure_unique_name = ensure_unique_name self.num_retries = num_retries self.replication_desired = replication_desired + self.put_threads = put_threads self.filename = filename self._state_lock = threading.Lock() self._state = None # Previous run state (file list & manifest) @@ -342,13 +385,19 @@ class ArvPutUploadJob(object): self._file_paths = [] # Files to be updated in remote collection self._stop_checkpointer = threading.Event() self._checkpointer = threading.Thread(target=self._update_task) + self._checkpointer.daemon = True self._update_task_time = update_time # How many seconds wait between update runs - self._files_to_upload = [] - self.logger = logging.getLogger('arvados.arv_put') + self._files_to_upload = FileUploadList(dry_run=dry_run) + self.logger = logger + self.dry_run = dry_run if not self.use_cache and self.resume: raise ArvPutArgumentConflict('resume cannot be True when use_cache is False') + # Check for obvious dry-run responses + if self.dry_run and (not self.use_cache or not self.resume): + raise ArvPutUploadIsPending() + # Load cached data if any and if needed self._setup_state(update_collection) @@ -356,12 +405,14 @@ class ArvPutUploadJob(object): """ Start supporting thread & file uploading """ - self._checkpointer.daemon = True - self._checkpointer.start() + if not self.dry_run: + 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 @@ -379,22 +430,33 @@ class ArvPutUploadJob(object): 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() # Actual file upload self._upload_files() finally: - # Stop the thread before doing anything else - self._stop_checkpointer.set() - self._checkpointer.join() - # Commit all pending blocks & one last _update() - self._local_collection.manifest_text() - self._update(final=True) + if not self.dry_run: + # Stop the thread before doing anything else + self._stop_checkpointer.set() + self._checkpointer.join() + # Commit all pending blocks & one last _update() + self._local_collection.manifest_text() + self._update(final=True) + if save_collection: + self.save_collection() if self.use_cache: self._cache_file.close() - if save_collection: - self.save_collection() def save_collection(self): if self.update: @@ -418,7 +480,7 @@ class ArvPutUploadJob(object): num_retries=self.num_retries) def destroy_cache(self): - if self.resume: + if self.use_cache: try: os.unlink(self._cache_filename) except OSError as error: @@ -454,14 +516,18 @@ class ArvPutUploadJob(object): with self._collection_lock: self.bytes_written = self._collection_size(self._local_collection) if self.use_cache: + if final: + manifest = self._local_collection.manifest_text() + else: + # Get the manifest text without comitting pending blocks + manifest = self._local_collection.manifest_text(strip=False, + normalize=False, + only_committed=True) # Update cache with self._state_lock: - if final: - self._state['manifest'] = self._local_collection.manifest_text() - else: - # Get the manifest text without comitting pending blocks - self._state['manifest'] = self._local_collection._get_manifest_text(".", strip=False, normalize=False, only_committed=True) - self._save_state() + self._state['manifest'] = manifest + if self.use_cache: + self._save_state() # Call the reporter, if any self.report_progress() @@ -586,9 +652,14 @@ class ArvPutUploadJob(object): if self.filename: md5.update(self.filename) cache_filename = md5.hexdigest() - self._cache_file = open(os.path.join( + cache_filepath = os.path.join( arv_cmd.make_home_conf_dir(self.CACHE_DIR, 0o700, 'raise'), - cache_filename), 'a+') + cache_filename) + if self.resume: + self._cache_file = open(cache_filepath, 'a+') + else: + # --no-resume means start with a empty cache file. + self._cache_file = open(cache_filepath, 'w+') self._cache_filename = self._cache_file.name self._lock_file(self._cache_file) self._cache_file.seek(0) @@ -607,7 +678,18 @@ class ArvPutUploadJob(object): # No cache file, set empty state 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) + self._local_collection = arvados.collection.Collection(self._state['manifest'], replication_desired=self.replication_desired, put_threads=self.put_threads) + + def collection_file_paths(self, col, path_prefix='.'): + """Return a list of file paths by recursively go through the entire collection `col`""" + file_paths = [] + for name, item in col.items(): + if isinstance(item, arvados.arvfile.ArvadosFile): + file_paths.append(os.path.join(path_prefix, name)) + elif isinstance(item, arvados.collection.Subcollection): + new_prefix = os.path.join(path_prefix, name) + file_paths += self.collection_file_paths(item, path_prefix=new_prefix) + return file_paths def _lock_file(self, fileobj): try: @@ -733,6 +815,7 @@ def desired_project_uuid(api_client, project_uuid, num_retries): def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): global api_client + logger = logging.getLogger('arvados.arv_put') args = parse_arguments(arguments) status = 0 if api_client is None: @@ -741,7 +824,10 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): # Determine the name to use if args.name: if args.stream or args.raw: - print >>stderr, "Cannot use --name with --stream or --raw" + logger.error("Cannot use --name with --stream or --raw") + sys.exit(1) + elif args.update_collection: + logger.error("Cannot use --name with --update-collection") sys.exit(1) collection_name = args.name else: @@ -751,7 +837,7 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): socket.gethostname()) if args.project_uuid and (args.stream or args.raw): - print >>stderr, "Cannot use --project-uuid with --stream or --raw" + logger.error("Cannot use --project-uuid with --stream or --raw") sys.exit(1) # Determine the parent project @@ -759,7 +845,7 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): project_uuid = desired_project_uuid(api_client, args.project_uuid, args.retries) except (apiclient_errors.Error, ValueError) as error: - print >>stderr, error + logger.error(error) sys.exit(1) if args.progress: @@ -780,41 +866,57 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): bytes_expected = bytes_expected, num_retries = args.retries, replication_desired = args.replication, + put_threads = args.threads, name = collection_name, owner_uuid = project_uuid, ensure_unique_name = True, - update_collection = args.update_collection) + update_collection = args.update_collection, + logger=logger, + dry_run=args.dry_run) except ResumeCacheConflict: - print >>stderr, "\n".join([ + logger.error("\n".join([ "arv-put: Another process is already uploading this data.", - " Use --no-cache if this is really what you want."]) + " Use --no-cache if this is really what you want."])) sys.exit(1) except CollectionUpdateError as error: - print >>stderr, "\n".join([ - "arv-put: %s" % str(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) # 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.update_collection and args.resume and writer.bytes_written > 0: - print >>stderr, "\n".join([ - "arv-put: Resuming previous upload from last checkpoint.", - " Use the --no-resume option to start over."]) + 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.", + " Use the --no-resume option to start over."])) - writer.report_progress() + if not args.dry_run: + writer.report_progress() output = None try: writer.start(save_collection=not(args.stream or args.raw)) except arvados.errors.ApiError as error: - print >>stderr, "\n".join([ - "arv-put: %s" % str(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. - print >>stderr + logger.info("\n") if args.stream: if args.normalize: @@ -826,15 +928,15 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): else: try: if args.update_collection: - print >>stderr, "Collection updated: '{}'".format(writer.collection_name()) + logger.info("Collection updated: '{}'".format(writer.collection_name())) else: - print >>stderr, "Collection saved as '{}'".format(writer.collection_name()) + logger.info("Collection saved as '{}'".format(writer.collection_name())) if args.portable_data_hash: output = writer.portable_data_hash() else: output = writer.manifest_locator() except apiclient_errors.Error as error: - print >>stderr, ( + logger.error( "arv-put: Error creating Collection on project: {}.".format( error)) status = 1