X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5d17dfc6124a19ff7c9ebce607699d3e3f415bad..1c7de9d85417202a48ea82409ab390dfcab7f2a5:/sdk/python/arvados/commands/put.py diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py index 496db86ab4..89753a2286 100644 --- a/sdk/python/arvados/commands/put.py +++ b/sdk/python/arvados/commands/put.py @@ -14,10 +14,14 @@ import hashlib import json import os import pwd +import time import signal import socket import sys import tempfile +import threading +import copy +import logging from apiclient import errors as apiclient_errors import arvados.commands._util as arv_cmd @@ -167,7 +171,9 @@ def parse_arguments(arguments): args = arg_parser.parse_args(arguments) if len(args.paths) == 0: - args.paths += ['/dev/stdin'] + args.paths = ['-'] + + args.paths = map(lambda x: "-" if x == "/dev/stdin" else x, args.paths) if len(args.paths) != 1 or os.path.isdir(args.paths[0]): if args.filename: @@ -182,9 +188,9 @@ def parse_arguments(arguments): args.progress = True if args.paths == ['-']: - args.paths = ['/dev/stdin'] + args.resume = False if not args.filename: - args.filename = '-' + args.filename = 'stdin' return args @@ -224,6 +230,23 @@ class ResumeCache(object): self.cache_file.seek(0) return json.load(self.cache_file) + def check_cache(self, api_client=None, num_retries=0): + try: + state = self.load() + locator = None + try: + if "_finished_streams" in state and len(state["_finished_streams"]) > 0: + locator = state["_finished_streams"][0][1][0] + elif "_current_stream_locators" in state and len(state["_current_stream_locators"]) > 0: + locator = state["_current_stream_locators"][0] + if locator is not None: + kc = arvados.keep.KeepClient(api_client=api_client) + kc.head(locator, num_retries=num_retries) + except Exception as e: + self.restart() + except (ValueError): + pass + def save(self, data): try: new_cache_fd, new_cache_name = tempfile.mkstemp( @@ -257,77 +280,344 @@ class ResumeCache(object): 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, **kwargs): - self.bytes_written = 0 - self._seen_inputs = [] - self.cache = cache +class ArvPutUploadJob(object): + CACHE_DIR = '.cache/arvados/arv-put' + EMPTY_STATE = { + 'manifest' : None, # Last saved manifest checkpoint + 'files' : {} # Previous run file list: {path : {size, mtime}} + } + + def __init__(self, paths, resume=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=60.0): + self.paths = paths + self.resume = resume self.reporter = reporter self.bytes_expected = bytes_expected - super(ArvPutCollectionWriter, self).__init__(**kwargs) - - @classmethod - def from_cache(cls, cache, reporter=None, bytes_expected=None, - num_retries=0, replication=0): + self.bytes_written = 0 + self.bytes_skipped = 0 + self.name = name + self.owner_uuid = owner_uuid + self.ensure_unique_name = ensure_unique_name + self.num_retries = num_retries + self.replication_desired = replication_desired + self.filename = filename + self._state_lock = threading.Lock() + self._state = None # Previous run state (file list & manifest) + self._current_files = [] # Current run file list + self._cache_file = None + self._collection = None + self._collection_lock = threading.Lock() + self._stop_checkpointer = threading.Event() + self._checkpointer = threading.Thread(target=self._update_task) + self._update_task_time = update_time # How many seconds wait between update runs + self.logger = logging.getLogger('arvados.arv_put') + # Load cached data if any and if needed + self._setup_state() + + def start(self): + """ + Start supporting thread & file uploading + """ + self._checkpointer.daemon = True + self._checkpointer.start() try: - state = cache.load() - state['_data_buffer'] = [base64.decodestring(state['_data_buffer'])] - writer = cls.from_state(state, cache, reporter, bytes_expected, - num_retries=num_retries, - replication=replication) - except (TypeError, ValueError, - arvados.errors.StaleWriterStateError) as error: - return cls(cache, reporter, bytes_expected, num_retries=num_retries) - else: - return writer - - def cache_state(self): - if self.cache is None: - return - 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) + for path in self.paths: + # Test for stdin first, in case some file named '-' exist + if path == '-': + self._write_stdin(self.filename or 'stdin') + elif os.path.isdir(path): + self._write_directory_tree(path) + else: + self._write_file(path, self.filename or os.path.basename(path)) + finally: + # Stop the thread before doing anything else + self._stop_checkpointer.set() + self._checkpointer.join() + # Commit all & one last _update() + self.manifest_text() + self._update() + if self.resume: + self._cache_file.close() + # Correct the final written bytes count + self.bytes_written -= self.bytes_skipped + + def save_collection(self): + with self._collection_lock: + self._my_collection().save_new( + name=self.name, owner_uuid=self.owner_uuid, + ensure_unique_name=self.ensure_unique_name, + num_retries=self.num_retries) + + def destroy_cache(self): + if self.resume: + try: + os.unlink(self._cache_filename) + except OSError as error: + # That's what we wanted anyway. + if error.errno != errno.ENOENT: + raise + self._cache_file.close() + + def _collection_size(self, collection): + """ + Recursively get the total size of the collection + """ + size = 0 + for item in collection.values(): + if isinstance(item, arvados.collection.Collection) or isinstance(item, arvados.collection.Subcollection): + size += self._collection_size(item) + else: + size += item.size() + return size + + def _update_task(self): + """ + Periodically called support task. File uploading is + asynchronous so we poll status from the collection. + """ + while not self._stop_checkpointer.wait(self._update_task_time): + self._update() + + def _update(self): + """ + Update cached manifest text and report progress. + """ + with self._collection_lock: + self.bytes_written = self._collection_size(self._my_collection()) + # Update cache, if resume enabled + if self.resume: + with self._state_lock: + # Get the manifest text without comitting pending blocks + self._state['manifest'] = self._my_collection()._get_manifest_text(".", strip=False, normalize=False, only_committed=True) + if self.resume: + self._save_state() + # Call the reporter, if any + self.report_progress() 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 / arvados.config.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 / arvados.config.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 _write_directory_tree(self, path, stream_name="."): + # TODO: Check what happens when multiple directories are passed as + # arguments. + # If the code below is uncommented, integration test + # test_ArvPutSignedManifest (tests.test_arv_put.ArvPutIntegrationTest) + # fails, I suppose it is because the manifest_uuid changes because + # of the dir addition to stream_name. + + # if stream_name == '.': + # stream_name = os.path.join('.', os.path.basename(path)) + for item in os.listdir(path): + if os.path.isdir(os.path.join(path, item)): + self._write_directory_tree(os.path.join(path, item), + os.path.join(stream_name, item)) + else: + self._write_file(os.path.join(path, item), + os.path.join(stream_name, item)) + + def _write_stdin(self, filename): + with self._collection_lock: + output = self._my_collection().open(filename, 'w') + self._write(sys.stdin, output) + output.close() + + def _write_file(self, source, filename): + resume_offset = 0 + if self.resume: + # Check if file was already uploaded (at least partially) + with self._collection_lock: + try: + file_in_collection = self._my_collection().find(filename) + except IOError: + # Not found + file_in_collection = None + # If no previous cached data on this file, store it for an eventual + # repeated run. + if source not in self._state['files']: + with self._state_lock: + self._state['files'][source] = { + 'mtime': os.path.getmtime(source), + 'size' : os.path.getsize(source) + } + with self._state_lock: + cached_file_data = self._state['files'][source] + # See if this file was already uploaded at least partially + if file_in_collection: + if cached_file_data['mtime'] == os.path.getmtime(source) and cached_file_data['size'] == os.path.getsize(source): + if cached_file_data['size'] == file_in_collection.size(): + # File already there, skip it. + self.bytes_skipped += cached_file_data['size'] + return + elif cached_file_data['size'] > file_in_collection.size(): + # File partially uploaded, resume! + resume_offset = file_in_collection.size() + else: + # Inconsistent cache, re-upload the file + self.logger.warning("Uploaded version of file '{}' is bigger than local version, will re-upload it from scratch.".format(source)) + else: + # Local file differs from cached data, re-upload it + pass + with open(source, 'r') as source_fd: + if resume_offset > 0: + # Start upload where we left off + with self._collection_lock: + output = self._my_collection().open(filename, 'a') + source_fd.seek(resume_offset) + self.bytes_skipped += resume_offset + else: + # Start from scratch + with self._collection_lock: + output = self._my_collection().open(filename, 'w') + self._write(source_fd, output) + output.close() + + def _write(self, source_fd, output): + first_read = True + while True: + data = source_fd.read(arvados.config.KEEP_BLOCK_SIZE) + # Allow an empty file to be written + if not data and not first_read: + break + if first_read: + first_read = False + output.write(data) + + def _my_collection(self): + """ + Create a new collection if none cached. Load it from cache otherwise. + """ + if self._collection is None: + with self._state_lock: + manifest = self._state['manifest'] + if self.resume and manifest is not None: + # Create collection from saved state + self._collection = arvados.collection.Collection( + manifest, + replication_desired=self.replication_desired) + else: + # Create new collection + self._collection = arvados.collection.Collection( + replication_desired=self.replication_desired) + return self._collection + + def _setup_state(self): + """ + Create a new cache file or load a previously existing one. + """ + if self.resume: + md5 = hashlib.md5() + md5.update(arvados.config.get('ARVADOS_API_HOST', '!nohost')) + realpaths = sorted(os.path.realpath(path) for path in self.paths) + md5.update('\0'.join(realpaths)) + if self.filename: + md5.update(self.filename) + cache_filename = md5.hexdigest() + self._cache_file = open(os.path.join( + arv_cmd.make_home_conf_dir(self.CACHE_DIR, 0o700, 'raise'), + cache_filename), 'a+') + self._cache_filename = self._cache_file.name + self._lock_file(self._cache_file) + self._cache_file.seek(0) + with self._state_lock: + try: + self._state = json.load(self._cache_file) + if not set(['manifest', 'files']).issubset(set(self._state.keys())): + # Cache at least partially incomplete, set up new cache + self._state = copy.deepcopy(self.EMPTY_STATE) + except ValueError: + # Cache file empty, set up new cache + self._state = copy.deepcopy(self.EMPTY_STATE) + # Load how many bytes were uploaded on previous run + with self._collection_lock: + self.bytes_written = self._collection_size(self._my_collection()) + # No resume required + else: + with self._state_lock: + self._state = copy.deepcopy(self.EMPTY_STATE) + + def _lock_file(self, fileobj): + try: + fcntl.flock(fileobj, fcntl.LOCK_EX | fcntl.LOCK_NB) + except IOError: + raise ResumeCacheConflict("{} locked".format(fileobj.name)) + + def _save_state(self): + """ + Atomically save current state into cache. + """ + try: + with self._state_lock: + state = self._state + new_cache_fd, new_cache_name = tempfile.mkstemp( + dir=os.path.dirname(self._cache_filename)) + self._lock_file(new_cache_fd) + new_cache = os.fdopen(new_cache_fd, 'r+') + json.dump(state, new_cache) + new_cache.flush() + os.fsync(new_cache) + os.rename(new_cache_name, self._cache_filename) + except (IOError, OSError, ResumeCacheConflict) as error: + self.logger.error("There was a problem while saving the cache file: {}".format(error)) + try: + os.unlink(new_cache_name) + except NameError: # mkstemp failed. + pass + else: + self._cache_file.close() + self._cache_file = new_cache + + def collection_name(self): + with self._collection_lock: + name = self._my_collection().api_response()['name'] if self._my_collection().api_response() else None + return name + + def manifest_locator(self): + with self._collection_lock: + locator = self._my_collection().manifest_locator() + return locator + + def portable_data_hash(self): + with self._collection_lock: + datahash = self._my_collection().portable_data_hash() + return datahash + + def manifest_text(self, stream_name=".", strip=False, normalize=False): + with self._collection_lock: + manifest = self._my_collection().manifest_text(stream_name, strip, normalize) + return manifest + + def _datablocks_on_item(self, item): + """ + Return a list of datablock locators, recursively navigating + through subcollections + """ + if isinstance(item, arvados.arvfile.ArvadosFile): + if item.size() == 0: + # Empty file locator + return ["d41d8cd98f00b204e9800998ecf8427e+0"] + else: + locators = [] + for segment in item.segments(): + loc = segment.locator + locators.append(loc) + return locators + elif isinstance(item, arvados.collection.Collection): + l = [self._datablocks_on_item(x) for x in item.values()] + # Fast list flattener method taken from: + # http://stackoverflow.com/questions/952914/making-a-flat-list-out-of-list-of-lists-in-python + return [loc for sublist in l for loc in sublist] + else: + return None + + def data_locators(self): + with self._collection_lock: + # Make sure all datablocks are flushed before getting the locators + self._my_collection().manifest_text() + datablocks = self._datablocks_on_item(self._my_collection()) + return datablocks def expected_bytes_for(pathlist): @@ -409,107 +699,62 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): print >>stderr, error sys.exit(1) - # write_copies diverges from args.replication here. - # args.replication is how many copies we will instruct Arvados to - # maintain (by passing it in collections().create()) after all - # data is written -- and if None was given, we'll use None there. - # Meanwhile, write_copies is how many copies of each data block we - # write to Keep, which has to be a number. - # - # If we simply changed args.replication from None to a default - # here, we'd end up erroneously passing the default replication - # level (instead of None) to collections().create(). - write_copies = (args.replication or - api_client._rootDesc.get('defaultCollectionReplication', 2)) - if args.progress: reporter = progress_writer(human_progress) elif args.batch_progress: reporter = progress_writer(machine_progress) else: reporter = None - bytes_expected = expected_bytes_for(args.paths) - - resume_cache = None - if args.resume: - try: - resume_cache = ResumeCache(ResumeCache.make_path(args)) - except (IOError, OSError, ValueError): - pass # Couldn't open cache directory/file. Continue without it. - except ResumeCacheConflict: - print >>stderr, "\n".join([ - "arv-put: Another process is already uploading this data.", - " Use --no-resume if this is really what you want."]) - sys.exit(1) - if resume_cache is None: - writer = ArvPutCollectionWriter( - resume_cache, reporter, bytes_expected, - num_retries=args.retries, - replication=write_copies) - else: - writer = ArvPutCollectionWriter.from_cache( - resume_cache, reporter, bytes_expected, - num_retries=args.retries, - replication=write_copies) + bytes_expected = expected_bytes_for(args.paths) + try: + writer = ArvPutUploadJob(paths = args.paths, + resume = args.resume, + filename = args.filename, + reporter = reporter, + bytes_expected = bytes_expected, + num_retries = args.retries, + replication_desired = args.replication, + name = collection_name, + owner_uuid = project_uuid, + ensure_unique_name = True) + except ResumeCacheConflict: + print >>stderr, "\n".join([ + "arv-put: Another process is already uploading this data.", + " Use --no-resume if this is really what you want."]) + sys.exit(1) # 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. + if 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."]) 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() - + output = None + writer.start() if args.progress: # Print newline to split stderr from stdout for humans. print >>stderr if args.stream: - output = writer.manifest_text() if args.normalize: - output = arvados.collection.CollectionReader(output).manifest_text(normalize=True) + output = writer.manifest_text(normalize=True) + else: + output = writer.manifest_text() elif args.raw: output = ','.join(writer.data_locators()) else: try: - manifest_text = writer.manifest_text() - if args.normalize: - manifest_text = arvados.collection.CollectionReader(manifest_text).manifest_text(normalize=True) - replication_attr = 'replication_desired' - if api_client._schema.schemas['Collection']['properties'].get(replication_attr, None) is None: - # API called it 'redundancy' before #3410. - replication_attr = 'redundancy' - # Register the resulting collection in Arvados. - collection = api_client.collections().create( - body={ - 'owner_uuid': project_uuid, - 'name': collection_name, - 'manifest_text': manifest_text, - replication_attr: args.replication, - }, - ensure_unique_name=True - ).execute(num_retries=args.retries) - - print >>stderr, "Collection saved as '%s'" % collection['name'] - - if args.portable_data_hash and 'portable_data_hash' in collection and collection['portable_data_hash']: - output = collection['portable_data_hash'] + writer.save_collection() + print >>stderr, "Collection saved as '%s'" % writer.collection_name() + if args.portable_data_hash: + output = writer.portable_data_hash() else: - output = collection['uuid'] - + output = writer.manifest_locator() except apiclient_errors.Error as error: print >>stderr, ( "arv-put: Error creating Collection on project: {}.".format( @@ -517,9 +762,12 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): status = 1 # Print the locator (uuid) of the new collection. - stdout.write(output) - if not output.endswith('\n'): - stdout.write('\n') + if output is None: + status = status or 1 + else: + stdout.write(output) + if not output.endswith('\n'): + stdout.write('\n') for sigcode, orig_handler in orig_signal_handlers.items(): signal.signal(sigcode, orig_handler) @@ -527,10 +775,10 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): if status != 0: sys.exit(status) - if resume_cache is not None: - resume_cache.destroy() - + # Success! + writer.destroy_cache() return output + if __name__ == '__main__': main()