X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/4406d50cdf2ae7b2c3e9846ddcf629ad535cf7fa..c7f445954df35959174761ba7b1f44ecf377c87a:/sdk/python/arvados/commands/put.py diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py index 8082752428..e4e1b6dad2 100644 --- a/sdk/python/arvados/commands/put.py +++ b/sdk/python/arvados/commands/put.py @@ -5,111 +5,136 @@ import argparse import arvados +import base64 +import errno +import fcntl +import hashlib +import json import os +import signal import sys +import tempfile + +import arvados.commands._util as arv_cmd + +CAUGHT_SIGNALS = [signal.SIGINT, signal.SIGQUIT, signal.SIGTERM] + +upload_opts = argparse.ArgumentParser(add_help=False) + +upload_opts.add_argument('paths', metavar='path', type=str, nargs='*', + help=""" +Local file or directory. Default: read from standard input. +""") + +upload_opts.add_argument('--max-manifest-depth', type=int, metavar='N', + default=-1, help=""" +Maximum depth of directory tree to represent in the manifest +structure. A directory structure deeper than this will be represented +as a single stream in the manifest. If N=0, the manifest will contain +a single stream. Default: -1 (unlimited), i.e., exactly one manifest +stream per filesystem directory that contains files. +""") + +_group = upload_opts.add_mutually_exclusive_group() + +_group.add_argument('--as-stream', action='store_true', dest='stream', + help=""" +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. +""") + +_group.add_argument('--as-manifest', action='store_true', dest='manifest', + help=""" +Synonym for --manifest. +""") + +_group.add_argument('--in-manifest', action='store_true', dest='manifest', + help=""" +Synonym for --manifest. +""") + +_group.add_argument('--manifest', action='store_true', + help=""" +Store the file data and resulting manifest in Keep, save a Collection +object in Arvados, and display the manifest locator (Collection uuid) +on stdout. This is the default behavior. +""") + +_group.add_argument('--as-raw', action='store_true', dest='raw', + help=""" +Synonym for --raw. +""") + +_group.add_argument('--raw', action='store_true', + help=""" +Store the file content and display the data block locators on stdout, +separated by commas, with a trailing newline. Do not store a +manifest. +""") + +upload_opts.add_argument('--use-filename', type=str, default=None, + dest='filename', help=""" +Synonym for --filename. +""") + +upload_opts.add_argument('--filename', type=str, default=None, + help=""" +Use the given filename in the manifest, instead of the name of the +local file. This is useful when "-" or "/dev/stdin" is given as an +input file. It can be used only if there is exactly one path given and +it is not a directory. Implies --manifest. +""") + +run_opts = argparse.ArgumentParser(add_help=False) +_group = run_opts.add_mutually_exclusive_group() +_group.add_argument('--progress', action='store_true', + help=""" +Display human-readable progress on stderr (bytes and, if possible, +percentage of total data size). This is the default behavior when +stderr is a tty. +""") + +_group.add_argument('--no-progress', action='store_true', + help=""" +Do not display human-readable progress on stderr, even if stderr is a +tty. +""") + +_group.add_argument('--batch-progress', action='store_true', + help=""" +Display machine-readable progress on stderr (bytes and, if known, +total data size). +""") + +_group = run_opts.add_mutually_exclusive_group() +_group.add_argument('--resume', action='store_true', default=True, + help=""" +Continue interrupted uploads from cached state (default). +""") +_group.add_argument('--no-resume', action='store_false', dest='resume', + help=""" +Do not continue interrupted uploads from cached state. +""") + +arg_parser = argparse.ArgumentParser( + description='Copy data from the local filesystem to Keep.', + parents=[upload_opts, run_opts]) def parse_arguments(arguments): - parser = argparse.ArgumentParser( - description='Copy data from the local filesystem to Keep.') - - parser.add_argument('paths', metavar='path', type=str, nargs='*', - help=""" - Local file or directory. Default: read from standard input. - """) - - parser.add_argument('--max-manifest-depth', type=int, metavar='N', - default=-1, help=""" - Maximum depth of directory tree to represent in the manifest - structure. A directory structure deeper than this will be represented - as a single stream in the manifest. If N=0, the manifest will contain - a single stream. Default: -1 (unlimited), i.e., exactly one manifest - stream per filesystem directory that contains files. - """) - - group = parser.add_mutually_exclusive_group() - - group.add_argument('--as-stream', action='store_true', dest='stream', - help=""" - 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. - """) - - group.add_argument('--as-manifest', action='store_true', dest='manifest', - help=""" - Synonym for --manifest. - """) - - group.add_argument('--in-manifest', action='store_true', dest='manifest', - help=""" - Synonym for --manifest. - """) - - group.add_argument('--manifest', action='store_true', - help=""" - Store the file data and resulting manifest in Keep, save a Collection - object in Arvados, and display the manifest locator (Collection uuid) - on stdout. This is the default behavior. - """) - - group.add_argument('--as-raw', action='store_true', dest='raw', - help=""" - Synonym for --raw. - """) - - group.add_argument('--raw', action='store_true', - help=""" - Store the file content and display the data block locators on stdout, - separated by commas, with a trailing newline. Do not store a - manifest. - """) - - parser.add_argument('--use-filename', type=str, default=None, - dest='filename', help=""" - Synonym for --filename. - """) - - parser.add_argument('--filename', type=str, default=None, - help=""" - Use the given filename in the manifest, instead of the name of the - local file. This is useful when "-" or "/dev/stdin" is given as an - input file. It can be used only if there is exactly one path given and - it is not a directory. Implies --manifest. - """) - - group = parser.add_mutually_exclusive_group() - group.add_argument('--progress', action='store_true', - help=""" - Display human-readable progress on stderr (bytes and, if possible, - percentage of total data size). This is the default behavior when - stderr is a tty. - """) - - group.add_argument('--no-progress', action='store_true', - help=""" - Do not display human-readable progress on stderr, even if stderr is a - tty. - """) - - group.add_argument('--batch-progress', action='store_true', - help=""" - Display machine-readable progress on stderr (bytes and, if known, - total data size). - """) - - args = parser.parse_args(arguments) + args = arg_parser.parse_args(arguments) if len(args.paths) == 0: args.paths += ['/dev/stdin'] if len(args.paths) != 1 or os.path.isdir(args.paths[0]): if args.filename: - parser.error(""" + arg_parser.error(""" --filename argument cannot be used when storing a directory or multiple files. """) @@ -126,82 +151,243 @@ def parse_arguments(arguments): return args -class CollectionWriterWithProgress(arvados.CollectionWriter): - def flush_data(self, *args, **kwargs): - if not getattr(self, 'display_type', None): +class ResumeCacheConflict(Exception): + pass + + +class ResumeCache(object): + CACHE_DIR = '.cache/arvados/arv-put' + + @classmethod + def setup_user_cache(cls): + return arv_cmd.make_home_conf_dir(cls.CACHE_DIR, 0o700) + + def __init__(self, file_spec): + self.cache_file = open(file_spec, 'a+') + self._lock_file(self.cache_file) + self.filename = self.cache_file.name + + @classmethod + def make_path(cls, args): + md5 = hashlib.md5() + md5.update(arvados.config.get('ARVADOS_API_HOST', '!nohost')) + realpaths = sorted(os.path.realpath(path) for path in args.paths) + md5.update('\0'.join(realpaths)) + if any(os.path.isdir(path) for path in realpaths): + md5.update(str(max(args.max_manifest_depth, -1))) + elif args.filename: + md5.update(args.filename) + return os.path.join(cls.CACHE_DIR, md5.hexdigest()) + + def _lock_file(self, fileobj): + try: + fcntl.flock(fileobj, fcntl.LOCK_EX | fcntl.LOCK_NB) + except IOError: + raise ResumeCacheConflict("{} locked".format(fileobj.name)) + + def load(self): + self.cache_file.seek(0) + return json.load(self.cache_file) + + def save(self, data): + try: + new_cache_fd, new_cache_name = tempfile.mkstemp( + dir=os.path.dirname(self.filename)) + self._lock_file(new_cache_fd) + 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: + try: + os.unlink(new_cache_name) + except NameError: # mkstemp failed. + pass + else: + self.cache_file.close() + self.cache_file = new_cache + + def close(self): + self.cache_file.close() + + def destroy(self): + try: + os.unlink(self.filename) + except OSError as error: + if error.errno != errno.ENOENT: # That's what we wanted anyway. + raise + self.close() + + def restart(self): + self.destroy() + self.__init__(self.filename) + + +class ArvPutCollectionWriter(arvados.ResumableCollectionWriter): + STATE_PROPS = (arvados.ResumableCollectionWriter.STATE_PROPS + + ['bytes_written', '_seen_inputs']) + + def __init__(self, cache=None, reporter=None, bytes_expected=None): + self.bytes_written = 0 + self._seen_inputs = [] + self.cache = cache + self.reporter = reporter + self.bytes_expected = bytes_expected + super(ArvPutCollectionWriter, self).__init__() + + @classmethod + def from_cache(cls, cache, reporter=None, bytes_expected=None): + try: + state = cache.load() + state['_data_buffer'] = [base64.decodestring(state['_data_buffer'])] + writer = cls.from_state(state, cache, reporter, bytes_expected) + except (TypeError, ValueError, + arvados.errors.StaleWriterStateError) as error: + return cls(cache, reporter, bytes_expected) + else: + return writer + + def cache_state(self): + if self.cache is None: return - if not hasattr(self, 'bytes_flushed'): - self.bytes_flushed = 0 - self.bytes_flushed += self._data_buffer_len - super(CollectionWriterWithProgress, self).flush_data(*args, **kwargs) - self.bytes_flushed -= self._data_buffer_len - if self.display_type == 'machine': - sys.stderr.write('%s %d: %d written %d total\n' % - (sys.argv[0], - os.getpid(), - self.bytes_flushed, - getattr(self, 'bytes_expected', -1))) - elif getattr(self, 'bytes_expected', 0) > 0: - pct = 100.0 * self.bytes_flushed / self.bytes_expected - sys.stderr.write('\r%dM / %dM %.1f%% ' % - (self.bytes_flushed >> 20, - self.bytes_expected >> 20, pct)) + state = self.dump_state() + # Transform attributes for serialization. + for attr, value in state.items(): + if attr == '_data_buffer': + state[attr] = base64.encodestring(''.join(value)) + elif hasattr(value, 'popleft'): + state[attr] = list(value) + self.cache.save(state) + + def report_progress(self): + if self.reporter is not None: + self.reporter(self.bytes_written, self.bytes_expected) + + def flush_data(self): + start_buffer_len = self._data_buffer_len + start_block_count = self.bytes_written / self.KEEP_BLOCK_SIZE + super(ArvPutCollectionWriter, self).flush_data() + if self._data_buffer_len < start_buffer_len: # We actually PUT data. + self.bytes_written += (start_buffer_len - self._data_buffer_len) + self.report_progress() + if (self.bytes_written / self.KEEP_BLOCK_SIZE) > start_block_count: + self.cache_state() + + def _record_new_input(self, input_type, source_name, dest_name): + # The key needs to be a list because that's what we'll get back + # from JSON deserialization. + key = [input_type, source_name, dest_name] + if key in self._seen_inputs: + return False + self._seen_inputs.append(key) + return True + + def write_file(self, source, filename=None): + if self._record_new_input('file', source, filename): + super(ArvPutCollectionWriter, self).write_file(source, filename) + + def write_directory_tree(self, + path, stream_name='.', max_manifest_depth=-1): + if self._record_new_input('directory', path, stream_name): + super(ArvPutCollectionWriter, self).write_directory_tree( + path, stream_name, max_manifest_depth) + + +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: - sys.stderr.write('\r%d ' % self.bytes_flushed) + bytesum += os.path.getsize(path) + return bytesum + +_machine_format = "{} {}: {{}} written {{}} total\n".format(sys.argv[0], + os.getpid()) +def machine_progress(bytes_written, bytes_expected): + return _machine_format.format( + bytes_written, -1 if (bytes_expected is None) else bytes_expected) + +def human_progress(bytes_written, bytes_expected): + if bytes_expected: + return "\r{}M / {}M {:.1%} ".format( + bytes_written >> 20, bytes_expected >> 20, + float(bytes_written) / bytes_expected) + else: + return "\r{} ".format(bytes_written) - def manifest_text(self, *args, **kwargs): - manifest_text = (super(CollectionWriterWithProgress, self) - .manifest_text(*args, **kwargs)) - if getattr(self, 'display_type', None): - if self.display_type == 'human': - sys.stderr.write('\n') - self.display_type = None - return manifest_text +def progress_writer(progress_func, outfile=sys.stderr): + def write_progress(bytes_written, bytes_expected): + outfile.write(progress_func(bytes_written, bytes_expected)) + return write_progress +def exit_signal_handler(sigcode, frame): + sys.exit(-sigcode) def main(arguments=None): args = parse_arguments(arguments) if args.progress: - writer = CollectionWriterWithProgress() - writer.display_type = 'human' + reporter = progress_writer(human_progress) elif args.batch_progress: - writer = CollectionWriterWithProgress() - writer.display_type = 'machine' + reporter = progress_writer(machine_progress) else: - writer = arvados.CollectionWriter() - - # Walk the given directory trees and stat files, adding up file sizes, - # so we can display progress as percent - writer.bytes_expected = 0 - for path in args.paths: - if os.path.isdir(path): - for filename in arvados.util.listdir_recursive(path): - writer.bytes_expected += os.path.getsize( - os.path.join(path, filename)) - elif not os.path.isfile(path): - del writer.bytes_expected - break - else: - writer.bytes_expected += os.path.getsize(path) - - # Copy file data to Keep. - for path in args.paths: + reporter = None + bytes_expected = expected_bytes_for(args.paths) + + resume_cache = None + try: + if ResumeCache.setup_user_cache() is not None: + resume_cache = ResumeCache(ResumeCache.make_path(args)) + except (IOError, OSError): + pass # Couldn't open cache directory/file. Continue without it. + except ResumeCacheConflict: + print "arv-put: Another process is already uploading this data." + sys.exit(1) + + if resume_cache is None: + writer = ArvPutCollectionWriter(resume_cache, reporter, bytes_expected) + else: + if not args.resume: + resume_cache.restart() + writer = ArvPutCollectionWriter.from_cache( + resume_cache, reporter, bytes_expected) + + # 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 writer.bytes_written > 0: # We're resuming a previous upload. + print >>sys.stderr, "\n".join([ + "arv-put: Resuming previous upload from last checkpoint.", + " Use the --no-resume option to start over."]) + writer.report_progress() + + writer.do_queued_work() # Do work resumed from cache. + for path in args.paths: # Copy file data to Keep. if os.path.isdir(path): writer.write_directory_tree( path, max_manifest_depth=args.max_manifest_depth) else: writer.start_new_stream() writer.write_file(path, args.filename or os.path.basename(path)) + writer.finish_current_stream() + + if args.progress: # Print newline to split stderr from stdout for humans. + print >>sys.stderr if args.stream: print writer.manifest_text(), elif args.raw: - writer.finish_current_stream() print ','.join(writer.data_locators()) else: # Register the resulting collection in Arvados. - arvados.api().collections().create( + collection = arvados.api().collections().create( body={ 'uuid': writer.finish(), 'manifest_text': writer.manifest_text(), @@ -209,7 +395,13 @@ def main(arguments=None): ).execute() # Print the locator (uuid) of the new collection. - print writer.finish() + print collection['uuid'] + + for sigcode, orig_handler in orig_signal_handlers.items(): + signal.signal(sigcode, orig_handler) + + if resume_cache is not None: + resume_cache.destroy() if __name__ == '__main__': main()