import functools import logging import os import re import errno from collections import deque from stat import * from .arvfile import ArvadosFileBase, split, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, BlockManager from keep import * from .stream import StreamReader, normalize_stream, locator_block_size from .ranges import Range, LocatorAndRange import config import errors import util _logger = logging.getLogger('arvados.collection') class CollectionBase(object): def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): pass def _my_keep(self): if self._keep_client is None: self._keep_client = KeepClient(api_client=self._api_client, num_retries=self.num_retries) return self._keep_client def stripped_manifest(self): """ Return the manifest for the current collection with all non-portable hints (i.e., permission signatures and other hints other than size hints) removed from the locators. """ raw = self.manifest_text() clean = [] for line in raw.split("\n"): fields = line.split() if fields: clean_fields = fields[:1] + [ (re.sub(r'\+[^\d][^\+]*', '', x) if re.match(util.keep_locator_pattern, x) else x) for x in fields[1:]] clean += [' '.join(clean_fields), "\n"] return ''.join(clean) class CollectionReader(CollectionBase): def __init__(self, manifest_locator_or_text, api_client=None, keep_client=None, num_retries=0): """Instantiate a CollectionReader. This class parses Collection manifests to provide a simple interface to read its underlying files. Arguments: * manifest_locator_or_text: One of a Collection UUID, portable data hash, or full manifest text. * api_client: The API client to use to look up Collections. If not provided, CollectionReader will build one from available Arvados configuration. * keep_client: The KeepClient to use to download Collection data. If not provided, CollectionReader will build one from available Arvados configuration. * num_retries: The default number of times to retry failed service requests. Default 0. You may change this value after instantiation, but note those changes may not propagate to related objects like the Keep client. """ self._api_client = api_client self._keep_client = keep_client self.num_retries = num_retries if re.match(util.keep_locator_pattern, manifest_locator_or_text): self._manifest_locator = manifest_locator_or_text self._manifest_text = None elif re.match(util.collection_uuid_pattern, manifest_locator_or_text): self._manifest_locator = manifest_locator_or_text self._manifest_text = None elif re.match(util.manifest_pattern, manifest_locator_or_text): self._manifest_text = manifest_locator_or_text self._manifest_locator = None else: raise errors.ArgumentError( "Argument to CollectionReader must be a manifest or a collection UUID") self._api_response = None self._streams = None def _populate_from_api_server(self): # As in KeepClient itself, we must wait until the last # possible moment to instantiate an API client, in order to # avoid tripping up clients that don't have access to an API # server. If we do build one, make sure our Keep client uses # it. If instantiation fails, we'll fall back to the except # clause, just like any other Collection lookup # failure. Return an exception, or None if successful. try: if self._api_client is None: self._api_client = arvados.api('v1') self._keep_client = None # Make a new one with the new api. self._api_response = self._api_client.collections().get( uuid=self._manifest_locator).execute( num_retries=self.num_retries) self._manifest_text = self._api_response['manifest_text'] return None except Exception as e: return e def _populate_from_keep(self): # Retrieve a manifest directly from Keep. This has a chance of # working if [a] the locator includes a permission signature # or [b] the Keep services are operating in world-readable # mode. Return an exception, or None if successful. try: self._manifest_text = self._my_keep().get( self._manifest_locator, num_retries=self.num_retries) except Exception as e: return e def _populate(self): error_via_api = None error_via_keep = None should_try_keep = ((self._manifest_text is None) and util.keep_locator_pattern.match( self._manifest_locator)) if ((self._manifest_text is None) and util.signed_locator_pattern.match(self._manifest_locator)): error_via_keep = self._populate_from_keep() if self._manifest_text is None: error_via_api = self._populate_from_api_server() if error_via_api is not None and not should_try_keep: raise error_via_api if ((self._manifest_text is None) and not error_via_keep and should_try_keep): # Looks like a keep locator, and we didn't already try keep above error_via_keep = self._populate_from_keep() if self._manifest_text is None: # Nothing worked! raise arvados.errors.NotFoundError( ("Failed to retrieve collection '{}' " + "from either API server ({}) or Keep ({})." ).format( self._manifest_locator, error_via_api, error_via_keep)) self._streams = [sline.split() for sline in self._manifest_text.split("\n") if sline] def _populate_first(orig_func): # Decorator for methods that read actual Collection data. @functools.wraps(orig_func) def wrapper(self, *args, **kwargs): if self._streams is None: self._populate() return orig_func(self, *args, **kwargs) return wrapper @_populate_first def api_response(self): """api_response() -> dict or None Returns information about this Collection fetched from the API server. If the Collection exists in Keep but not the API server, currently returns None. Future versions may provide a synthetic response. """ return self._api_response @_populate_first def normalize(self): # Rearrange streams streams = {} for s in self.all_streams(): for f in s.all_files(): streamname, filename = split(s.name() + "/" + f.name()) if streamname not in streams: streams[streamname] = {} if filename not in streams[streamname]: streams[streamname][filename] = [] for r in f.segments: streams[streamname][filename].extend(s.locators_and_ranges(r.locator, r.range_size)) self._streams = [normalize_stream(s, streams[s]) for s in sorted(streams)] # Regenerate the manifest text based on the normalized streams self._manifest_text = ''.join( [StreamReader(stream, keep=self._my_keep()).manifest_text() for stream in self._streams]) @_populate_first def open(self, streampath, filename=None): """open(streampath[, filename]) -> file-like object Pass in the path of a file to read from the Collection, either as a single string or as two separate stream name and file name arguments. This method returns a file-like object to read that file. """ if filename is None: streampath, filename = split(streampath) keep_client = self._my_keep() for stream_s in self._streams: stream = StreamReader(stream_s, keep_client, num_retries=self.num_retries) if stream.name() == streampath: break else: raise ValueError("stream '{}' not found in Collection". format(streampath)) try: return stream.files()[filename] except KeyError: raise ValueError("file '{}' not found in Collection stream '{}'". format(filename, streampath)) @_populate_first def all_streams(self): return [StreamReader(s, self._my_keep(), num_retries=self.num_retries) for s in self._streams] def all_files(self): for s in self.all_streams(): for f in s.all_files(): yield f @_populate_first def manifest_text(self, strip=False, normalize=False): if normalize: cr = CollectionReader(self.manifest_text()) cr.normalize() return cr.manifest_text(strip=strip, normalize=False) elif strip: return self.stripped_manifest() else: return self._manifest_text class _WriterFile(ArvadosFileBase): def __init__(self, coll_writer, name): super(_WriterFile, self).__init__(name, 'wb') self.dest = coll_writer def close(self): super(_WriterFile, self).close() self.dest.finish_current_file() @ArvadosFileBase._before_close def write(self, data): self.dest.write(data) @ArvadosFileBase._before_close def writelines(self, seq): for data in seq: self.write(data) @ArvadosFileBase._before_close def flush(self): self.dest.flush_data() class CollectionWriter(CollectionBase): def __init__(self, api_client=None, num_retries=0): """Instantiate a CollectionWriter. CollectionWriter lets you build a new Arvados Collection from scratch. Write files to it. The CollectionWriter will upload data to Keep as appropriate, and provide you with the Collection manifest text when you're finished. Arguments: * api_client: The API client to use to look up Collections. If not provided, CollectionReader will build one from available Arvados configuration. * num_retries: The default number of times to retry failed service requests. Default 0. You may change this value after instantiation, but note those changes may not propagate to related objects like the Keep client. """ self._api_client = api_client self.num_retries = num_retries self._keep_client = None self._data_buffer = [] self._data_buffer_len = 0 self._current_stream_files = [] self._current_stream_length = 0 self._current_stream_locators = [] self._current_stream_name = '.' self._current_file_name = None self._current_file_pos = 0 self._finished_streams = [] self._close_file = None self._queued_file = None self._queued_dirents = deque() self._queued_trees = deque() self._last_open = None def __exit__(self, exc_type, exc_value, traceback): if exc_type is None: self.finish() def do_queued_work(self): # The work queue consists of three pieces: # * _queued_file: The file object we're currently writing to the # Collection. # * _queued_dirents: Entries under the current directory # (_queued_trees[0]) that we want to write or recurse through. # This may contain files from subdirectories if # max_manifest_depth == 0 for this directory. # * _queued_trees: Directories that should be written as separate # streams to the Collection. # This function handles the smallest piece of work currently queued # (current file, then current directory, then next directory) until # no work remains. The _work_THING methods each do a unit of work on # THING. _queue_THING methods add a THING to the work queue. while True: if self._queued_file: self._work_file() elif self._queued_dirents: self._work_dirents() elif self._queued_trees: self._work_trees() else: break def _work_file(self): while True: buf = self._queued_file.read(config.KEEP_BLOCK_SIZE) if not buf: break self.write(buf) self.finish_current_file() if self._close_file: self._queued_file.close() self._close_file = None self._queued_file = None def _work_dirents(self): path, stream_name, max_manifest_depth = self._queued_trees[0] if stream_name != self.current_stream_name(): self.start_new_stream(stream_name) while self._queued_dirents: dirent = self._queued_dirents.popleft() target = os.path.join(path, dirent) if os.path.isdir(target): self._queue_tree(target, os.path.join(stream_name, dirent), max_manifest_depth - 1) else: self._queue_file(target, dirent) break if not self._queued_dirents: self._queued_trees.popleft() def _work_trees(self): path, stream_name, max_manifest_depth = self._queued_trees[0] d = util.listdir_recursive( path, max_depth = (None if max_manifest_depth == 0 else 0)) if d: self._queue_dirents(stream_name, d) else: self._queued_trees.popleft() def _queue_file(self, source, filename=None): assert (self._queued_file is None), "tried to queue more than one file" if not hasattr(source, 'read'): source = open(source, 'rb') self._close_file = True else: self._close_file = False if filename is None: filename = os.path.basename(source.name) self.start_new_file(filename) self._queued_file = source def _queue_dirents(self, stream_name, dirents): assert (not self._queued_dirents), "tried to queue more than one tree" self._queued_dirents = deque(sorted(dirents)) def _queue_tree(self, path, stream_name, max_manifest_depth): self._queued_trees.append((path, stream_name, max_manifest_depth)) def write_file(self, source, filename=None): self._queue_file(source, filename) self.do_queued_work() def write_directory_tree(self, path, stream_name='.', max_manifest_depth=-1): self._queue_tree(path, stream_name, max_manifest_depth) self.do_queued_work() def write(self, newdata): if hasattr(newdata, '__iter__'): for s in newdata: self.write(s) return self._data_buffer.append(newdata) self._data_buffer_len += len(newdata) self._current_stream_length += len(newdata) while self._data_buffer_len >= config.KEEP_BLOCK_SIZE: self.flush_data() def open(self, streampath, filename=None): """open(streampath[, filename]) -> file-like object Pass in the path of a file to write to the Collection, either as a single string or as two separate stream name and file name arguments. This method returns a file-like object you can write to add it to the Collection. You may only have one file object from the Collection open at a time, so be sure to close the object when you're done. Using the object in a with statement makes that easy:: with cwriter.open('./doc/page1.txt') as outfile: outfile.write(page1_data) with cwriter.open('./doc/page2.txt') as outfile: outfile.write(page2_data) """ if filename is None: streampath, filename = split(streampath) if self._last_open and not self._last_open.closed: raise errors.AssertionError( "can't open '{}' when '{}' is still open".format( filename, self._last_open.name)) if streampath != self.current_stream_name(): self.start_new_stream(streampath) self.set_current_file_name(filename) self._last_open = _WriterFile(self, filename) return self._last_open def flush_data(self): data_buffer = ''.join(self._data_buffer) if data_buffer: self._current_stream_locators.append( self._my_keep().put(data_buffer[0:config.KEEP_BLOCK_SIZE])) self._data_buffer = [data_buffer[config.KEEP_BLOCK_SIZE:]] self._data_buffer_len = len(self._data_buffer[0]) def start_new_file(self, newfilename=None): self.finish_current_file() self.set_current_file_name(newfilename) def set_current_file_name(self, newfilename): if re.search(r'[\t\n]', newfilename): raise errors.AssertionError( "Manifest filenames cannot contain whitespace: %s" % newfilename) elif re.search(r'\x00', newfilename): raise errors.AssertionError( "Manifest filenames cannot contain NUL characters: %s" % newfilename) self._current_file_name = newfilename def current_file_name(self): return self._current_file_name def finish_current_file(self): if self._current_file_name is None: if self._current_file_pos == self._current_stream_length: return raise errors.AssertionError( "Cannot finish an unnamed file " + "(%d bytes at offset %d in '%s' stream)" % (self._current_stream_length - self._current_file_pos, self._current_file_pos, self._current_stream_name)) self._current_stream_files.append([ self._current_file_pos, self._current_stream_length - self._current_file_pos, self._current_file_name]) self._current_file_pos = self._current_stream_length self._current_file_name = None def start_new_stream(self, newstreamname='.'): self.finish_current_stream() self.set_current_stream_name(newstreamname) def set_current_stream_name(self, newstreamname): if re.search(r'[\t\n]', newstreamname): raise errors.AssertionError( "Manifest stream names cannot contain whitespace") self._current_stream_name = '.' if newstreamname=='' else newstreamname def current_stream_name(self): return self._current_stream_name def finish_current_stream(self): self.finish_current_file() self.flush_data() if not self._current_stream_files: pass elif self._current_stream_name is None: raise errors.AssertionError( "Cannot finish an unnamed stream (%d bytes in %d files)" % (self._current_stream_length, len(self._current_stream_files))) else: if not self._current_stream_locators: self._current_stream_locators.append(config.EMPTY_BLOCK_LOCATOR) self._finished_streams.append([self._current_stream_name, self._current_stream_locators, self._current_stream_files]) self._current_stream_files = [] self._current_stream_length = 0 self._current_stream_locators = [] self._current_stream_name = None self._current_file_pos = 0 self._current_file_name = None def finish(self): # Store the manifest in Keep and return its locator. return self._my_keep().put(self.manifest_text()) def portable_data_hash(self): stripped = self.stripped_manifest() return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped)) def manifest_text(self): self.finish_current_stream() manifest = '' for stream in self._finished_streams: if not re.search(r'^\.(/.*)?$', stream[0]): manifest += './' manifest += stream[0].replace(' ', '\\040') manifest += ' ' + ' '.join(stream[1]) manifest += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2]) manifest += "\n" return manifest def data_locators(self): ret = [] for name, locators, files in self._finished_streams: ret += locators return ret class ResumableCollectionWriter(CollectionWriter): STATE_PROPS = ['_current_stream_files', '_current_stream_length', '_current_stream_locators', '_current_stream_name', '_current_file_name', '_current_file_pos', '_close_file', '_data_buffer', '_dependencies', '_finished_streams', '_queued_dirents', '_queued_trees'] def __init__(self, api_client=None, num_retries=0): self._dependencies = {} super(ResumableCollectionWriter, self).__init__( api_client, num_retries=num_retries) @classmethod def from_state(cls, state, *init_args, **init_kwargs): # Try to build a new writer from scratch with the given state. # If the state is not suitable to resume (because files have changed, # been deleted, aren't predictable, etc.), raise a # StaleWriterStateError. Otherwise, return the initialized writer. # The caller is responsible for calling writer.do_queued_work() # appropriately after it's returned. writer = cls(*init_args, **init_kwargs) for attr_name in cls.STATE_PROPS: attr_value = state[attr_name] attr_class = getattr(writer, attr_name).__class__ # Coerce the value into the same type as the initial value, if # needed. if attr_class not in (type(None), attr_value.__class__): attr_value = attr_class(attr_value) setattr(writer, attr_name, attr_value) # Check dependencies before we try to resume anything. if any(KeepLocator(ls).permission_expired() for ls in writer._current_stream_locators): raise errors.StaleWriterStateError( "locators include expired permission hint") writer.check_dependencies() if state['_current_file'] is not None: path, pos = state['_current_file'] try: writer._queued_file = open(path, 'rb') writer._queued_file.seek(pos) except IOError as error: raise errors.StaleWriterStateError( "failed to reopen active file {}: {}".format(path, error)) return writer def check_dependencies(self): for path, orig_stat in self._dependencies.items(): if not S_ISREG(orig_stat[ST_MODE]): raise errors.StaleWriterStateError("{} not file".format(path)) try: now_stat = tuple(os.stat(path)) except OSError as error: raise errors.StaleWriterStateError( "failed to stat {}: {}".format(path, error)) if ((not S_ISREG(now_stat[ST_MODE])) or (orig_stat[ST_MTIME] != now_stat[ST_MTIME]) or (orig_stat[ST_SIZE] != now_stat[ST_SIZE])): raise errors.StaleWriterStateError("{} changed".format(path)) def dump_state(self, copy_func=lambda x: x): state = {attr: copy_func(getattr(self, attr)) for attr in self.STATE_PROPS} if self._queued_file is None: state['_current_file'] = None else: state['_current_file'] = (os.path.realpath(self._queued_file.name), self._queued_file.tell()) return state def _queue_file(self, source, filename=None): try: src_path = os.path.realpath(source) except Exception: raise errors.AssertionError("{} not a file path".format(source)) try: path_stat = os.stat(src_path) except OSError as stat_error: path_stat = None super(ResumableCollectionWriter, self)._queue_file(source, filename) fd_stat = os.fstat(self._queued_file.fileno()) if not S_ISREG(fd_stat.st_mode): # We won't be able to resume from this cache anyway, so don't # worry about further checks. self._dependencies[source] = tuple(fd_stat) elif path_stat is None: raise errors.AssertionError( "could not stat {}: {}".format(source, stat_error)) elif path_stat.st_ino != fd_stat.st_ino: raise errors.AssertionError( "{} changed between open and stat calls".format(source)) else: self._dependencies[src_path] = tuple(fd_stat) def write(self, data): if self._queued_file is None: raise errors.AssertionError( "resumable writer can't accept unsourced data") return super(ResumableCollectionWriter, self).write(data) class Collection(CollectionBase): """An abstract Arvados collection, consisting of a set of files and sub-collections. """ SYNC_READONLY = 1 SYNC_EXPLICIT = 2 SYNC_LIVE = 3 def __init__(self, manifest_locator_or_text=None, parent=None, api_client=None, keep_client=None, num_retries=0, block_manager=None, sync=Collection.SYNC_READONLY): """:manifest_locator_or_text: One of Arvados collection UUID, block locator of a manifest, raw manifest text, or None (to create an empty collection). :parent: the parent Collection, may be None. :api_client: The API client object to use for requests. If None, use default. :keep_client: the Keep client to use for requests. If None, use default. :num_retries: the number of retries for API and Keep requests. :block_manager: the block manager to use. If None, use parent's block manager or create one. :sync: Desired synchronization policy with API server collection record. :SYNC_READONLY: Collection is read only. No synchronization. This mode will also forego locking, which gives better performance. :SYNC_EXPLICIT: Synchronize on explicit request via `merge()` or `save()` :SYNC_LIVE: Synchronize with server in response to background websocket events, on block write, or on file close. """ self.parent = parent self._items = None self._api_client = api_client self._keep_client = keep_client self._block_manager = block_manager self.num_retries = num_retries self._manifest_locator = None self._manifest_text = None self._api_response = None if manifest_locator_or_text: if re.match(util.keep_locator_pattern, manifest_locator_or_text): self._manifest_locator = manifest_locator_or_text elif re.match(util.collection_uuid_pattern, manifest_locator_or_text): self._manifest_locator = manifest_locator_or_text elif re.match(util.manifest_pattern, manifest_locator_or_text): self._manifest_text = manifest_locator_or_text else: raise errors.ArgumentError( "Argument to CollectionReader must be a manifest or a collection UUID") def _my_api(self): if self._api_client is None: if self.parent is not None: return self.parent._my_api() self._api_client = arvados.api('v1') self._keep_client = None # Make a new one with the new api. return self._api_client def _my_keep(self): if self._keep_client is None: if self.parent is not None: return self.parent._my_keep() self._keep_client = KeepClient(api_client=self._my_api(), num_retries=self.num_retries) return self._keep_client def _my_block_manager(self): if self._block_manager is None: if self.parent is not None: return self.parent._my_block_manager() self._block_manager = BlockManager(self._my_keep()) return self._block_manager def _populate_from_api_server(self): # As in KeepClient itself, we must wait until the last # possible moment to instantiate an API client, in order to # avoid tripping up clients that don't have access to an API # server. If we do build one, make sure our Keep client uses # it. If instantiation fails, we'll fall back to the except # clause, just like any other Collection lookup # failure. Return an exception, or None if successful. try: self._api_response = self._my_api().collections().get( uuid=self._manifest_locator).execute( num_retries=self.num_retries) self._manifest_text = self._api_response['manifest_text'] return None except Exception as e: return e def _populate_from_keep(self): # Retrieve a manifest directly from Keep. This has a chance of # working if [a] the locator includes a permission signature # or [b] the Keep services are operating in world-readable # mode. Return an exception, or None if successful. try: self._manifest_text = self._my_keep().get( self._manifest_locator, num_retries=self.num_retries) except Exception as e: return e def _populate(self): self._items = {} if self._manifest_locator is None and self._manifest_text is None: return error_via_api = None error_via_keep = None should_try_keep = ((self._manifest_text is None) and util.keep_locator_pattern.match( self._manifest_locator)) if ((self._manifest_text is None) and util.signed_locator_pattern.match(self._manifest_locator)): error_via_keep = self._populate_from_keep() if self._manifest_text is None: error_via_api = self._populate_from_api_server() if error_via_api is not None and not should_try_keep: raise error_via_api if ((self._manifest_text is None) and not error_via_keep and should_try_keep): # Looks like a keep locator, and we didn't already try keep above error_via_keep = self._populate_from_keep() if self._manifest_text is None: # Nothing worked! raise arvados.errors.NotFoundError( ("Failed to retrieve collection '{}' " + "from either API server ({}) or Keep ({})." ).format( self._manifest_locator, error_via_api, error_via_keep)) # populate import_manifest(self._manifest_text, self) def _populate_first(orig_func): # Decorator for methods that read actual Collection data. @functools.wraps(orig_func) def wrapper(self, *args, **kwargs): if self._items is None: self._populate() return orig_func(self, *args, **kwargs) return wrapper def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): """Support scoped auto-commit in a with: block""" self.save(no_locator=True) if self._block_manager is not None: self._block_manager.stop_threads() @_populate_first def find(self, path, create=False, create_collection=False): """Recursively search the specified file path. May return either a Collection or ArvadosFile. :create: If true, create path components (i.e. Collections) that are missing. If "create" is False, return None if a path component is not found. :create_collection: If the path is not found, "create" is True, and "create_collection" is False, then create and return a new ArvadosFile for the last path component. If "create_collection" is True, then create and return a new Collection for the last path component. """ p = path.split("/") if p[0] == '.': del p[0] if len(p) > 0: item = self._items.get(p[0]) if len(p) == 1: # item must be a file if item is None and create: # create new file if create_collection: item = Collection(parent=self, num_retries=self.num_retries) else: item = ArvadosFile(self) self._items[p[0]] = item return item else: if item is None and create: # create new collection item = Collection(parent=self, num_retries=self.num_retries) self._items[p[0]] = item del p[0] return item.find("/".join(p), create=create) else: return self @_populate_first def api_response(self): """ api_response() -> dict or None Returns information about this Collection fetched from the API server. If the Collection exists in Keep but not the API server, currently returns None. Future versions may provide a synthetic response. """ return self._api_response def open(self, path, mode): """Open a file-like object for access. :path: path to a file in the collection :mode: one of "r", "r+", "w", "w+", "a", "a+" :"r": opens for reading :"r+": opens for reading and writing. Reads/writes share a file pointer. :"w", "w+": truncates to 0 and opens for reading and writing. Reads/writes share a file pointer. :"a", "a+": opens for reading and writing. All writes are appended to the end of the file. Writing does not affect the file pointer for reading. """ mode = mode.replace("b", "") if len(mode) == 0 or mode[0] not in ("r", "w", "a"): raise ArgumentError("Bad mode '%s'" % mode) create = (mode != "r") f = self.find(path, create=create) if f is None: raise IOError((errno.ENOENT, "File not found")) if not isinstance(f, ArvadosFile): raise IOError((errno.EISDIR, "Path must refer to a file.")) if mode[0] == "w": f.truncate(0) if mode == "r": return ArvadosFileReader(f, path, mode) else: return ArvadosFileWriter(f, path, mode) @_populate_first def modified(self): """Test if the collection (or any subcollection or file) has been modified since it was created.""" for k,v in self._items.items(): if v.modified(): return True return False @_populate_first def set_unmodified(self): """Recursively clear modified flag""" for k,v in self._items.items(): v.set_unmodified() @_populate_first def __iter__(self): """Iterate over names of files and collections contained in this collection.""" return self._items.iterkeys() @_populate_first def iterkeys(self): """Iterate over names of files and collections directly contained in this collection.""" return self._items.iterkeys() @_populate_first def __getitem__(self, k): """Get a file or collection that is directly contained by this collection. Use find() for path serach.""" return self._items[k] @_populate_first def __contains__(self, k): """If there is a file or collection a directly contained by this collection with name "k".""" return k in self._items @_populate_first def __len__(self): """Get the number of items directly contained in this collection""" return len(self._items) @_populate_first def __delitem__(self, p): """Delete an item by name which is directly contained by this collection.""" del self._items[p] @_populate_first def keys(self): """Get a list of names of files and collections directly contained in this collection.""" return self._items.keys() @_populate_first def values(self): """Get a list of files and collection objects directly contained in this collection.""" return self._items.values() @_populate_first def items(self): """Get a list of (name, object) tuples directly contained in this collection.""" return self._items.items() @_populate_first def exists(self, path): """Test if there is a file or collection at "path" """ return self.find(path) != None @_populate_first def remove(self, path): """Test if there is a file or collection at "path" """ p = path.split("/") if p[0] == '.': del p[0] if len(p) > 0: item = self._items.get(p[0]) if item is None: raise IOError((errno.ENOENT, "File not found")) if len(p) == 1: del self._items[p[0]] else: del p[0] item.remove("/".join(p)) else: raise IOError((errno.ENOENT, "File not found")) @_populate_first def manifest_text(self, strip=False, normalize=False): """Get the manifest text for this collection, sub collections and files. :strip: If True, remove signing tokens from block locators if present. If False, block locators are left unchanged. :normalize: If True, always export the manifest text in normalized form even if the Collection is not modified. If False and the collection is not modified, return the original manifest text even if it is not in normalized form. """ if self.modified() or self._manifest_text is None or normalize: return export_manifest(self, stream_name=".", portable_locators=strip) else: if strip: return self.stripped_manifest() else: return self._manifest_text def portable_data_hash(self): """Get the portable data hash for this collection's manifest.""" stripped = self.manifest_text(strip=True) return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped)) @_populate_first def save(self, no_locator=False): """Commit pending buffer blocks to Keep, write the manifest to Keep, and update the collection record to Keep. :no_locator: If False and there is no collection uuid associated with this Collection, raise an error. If True, do not raise an error. """ if self.modified(): self._my_block_manager().commit_all() self._my_keep().put(self.manifest_text(strip=True)) if self._manifest_locator is not None and re.match(util.collection_uuid_pattern, self._manifest_locator): self._api_response = self._my_api().collections().update( uuid=self._manifest_locator, body={'manifest_text': self.manifest_text(strip=False)} ).execute( num_retries=self.num_retries) elif not no_locator: raise AssertionError("Collection manifest_locator must be a collection uuid. Use save_as() for new collections.") self.set_unmodified() @_populate_first def save_as(self, name, owner_uuid=None, ensure_unique_name=False): """Save a new collection record. :name: The collection name. :owner_uuid: the user, or project uuid that will own this collection. If None, defaults to the current user. :ensure_unique_name: If True, ask the API server to rename the collection if it conflicts with a collection with the same name and owner. If False, a name conflict will result in an error. """ self._my_block_manager().commit_all() self._my_keep().put(self.manifest_text(strip=True)) body = {"manifest_text": self.manifest_text(strip=False), "name": name} if owner_uuid: body["owner_uuid"] = owner_uuid self._api_response = self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=self.num_retries) self._manifest_locator = self._api_response["uuid"] self.set_unmodified() def import_manifest(manifest_text, into_collection=None, api_client=None, keep=None, num_retries=None): """Import a manifest into a `Collection`. :manifest_text: The manifest text to import from. :into_collection: The `Collection` that will be initialized (must be empty). If None, create a new `Collection` object. :api_client: The API client object that will be used when creating a new `Collection` object. :keep: The keep client object that will be used when creating a new `Collection` object. num_retries the default number of api client and keep retries on error. """ if into_collection is not None: if len(into_collection) > 0: raise ArgumentError("Can only import manifest into an empty collection") c = into_collection else: c = Collection(api_client=api_client, keep_client=keep, num_retries=num_retries) STREAM_NAME = 0 BLOCKS = 1 SEGMENTS = 2 stream_name = None state = STREAM_NAME for n in re.finditer(r'(\S+)(\s+|$)', manifest_text): tok = n.group(1) sep = n.group(2) if state == STREAM_NAME: # starting a new stream stream_name = tok.replace('\\040', ' ') blocks = [] segments = [] streamoffset = 0L state = BLOCKS continue if state == BLOCKS: s = re.match(r'[0-9a-f]{32}\+(\d+)(\+\S+)*', tok) if s: blocksize = long(s.group(1)) blocks.append(Range(tok, streamoffset, blocksize)) streamoffset += blocksize else: state = SEGMENTS if state == SEGMENTS: s = re.search(r'^(\d+):(\d+):(\S+)', tok) if s: pos = long(s.group(1)) size = long(s.group(2)) name = s.group(3).replace('\\040', ' ') f = c.find("%s/%s" % (stream_name, name), create=True) f.add_segment(blocks, pos, size) else: # error! raise errors.SyntaxError("Invalid manifest format") if sep == "\n": stream_name = None state = STREAM_NAME c.set_unmodified() return c def export_manifest(item, stream_name=".", portable_locators=False): """ :item: Create a manifest for `item` (must be a `Collection` or `ArvadosFile`). If `item` is a is a `Collection`, this will also export subcollections. :stream_name: the name of the stream when exporting `item`. :portable_locators: If True, strip any permission hints on block locators. If False, use block locators as-is. """ buf = "" if isinstance(item, Collection): stream = {} sorted_keys = sorted(item.keys()) for k in [s for s in sorted_keys if isinstance(item[s], ArvadosFile)]: v = item[k] st = [] for s in v.segments: loc = s.locator if loc.startswith("bufferblock"): loc = v.parent._my_block_manager()._bufferblocks[loc].locator() if portable_locators: loc = KeepLocator(loc).stripped() st.append(LocatorAndRange(loc, locator_block_size(loc), s.segment_offset, s.range_size)) stream[k] = st if stream: buf += ' '.join(normalize_stream(stream_name, stream)) buf += "\n" for k in [s for s in sorted_keys if isinstance(item[s], Collection)]: buf += export_manifest(item[k], stream_name=os.path.join(stream_name, k), portable_locators=portable_locators) elif isinstance(item, ArvadosFile): st = [] for s in item.segments: loc = s.locator if loc.startswith("bufferblock"): loc = item._bufferblocks[loc].calculate_locator() if portable_locators: loc = KeepLocator(loc).stripped() st.append(LocatorAndRange(loc, locator_block_size(loc), s.segment_offset, s.range_size)) stream[stream_name] = st buf += ' '.join(normalize_stream(stream_name, stream)) buf += "\n" return buf