import functools import logging import os import re import errno import hashlib import time import threading from collections import deque from stat import * from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, _BlockManager, synchronized, must_be_writable, NoopLock from keep import KeepLocator, KeepClient from .stream import StreamReader from ._normalize_stream import normalize_stream from ._ranges import Range, LocatorAndRange from .safeapi import ThreadSafeApiCache import config import errors import util import events from arvados.retry import retry_method _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): """Get the manifest with locator hints stripped. 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 _WriterFile(_FileLikeObjectBase): 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() @_FileLikeObjectBase._before_close def write(self, data): self.dest.write(data) @_FileLikeObjectBase._before_close def writelines(self, seq): for data in seq: self.write(data) @_FileLikeObjectBase._before_close def flush(self): self.dest.flush_data() class CollectionWriter(CollectionBase): def __init__(self, api_client=None, num_retries=0, replication=None): """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. * replication: The number of copies of each block to store. If this argument is None or not supplied, replication is the server-provided default if available, otherwise 2. """ self._api_client = api_client self.num_retries = num_retries self.replication = (2 if replication is None else replication) 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], copies=self.replication)) 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: '%s'" % (newstreamname)) 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. This is useful for storing manifest fragments (task outputs) temporarily in Keep during a Crunch job. In other cases you should make a collection instead, by sending manifest_text() to the API server's "create collection" endpoint. """ return self._my_keep().put(self.manifest_text(), copies=self.replication) 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, **kwargs): self._dependencies = {} super(ResumableCollectionWriter, self).__init__(api_client, **kwargs) @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) ADD = "add" DEL = "del" MOD = "mod" TOK = "tok" FILE = "file" COLLECTION = "collection" class RichCollectionBase(CollectionBase): """Base class for Collections and Subcollections. Implements the majority of functionality relating to accessing items in the Collection. """ def __init__(self, parent=None): self.parent = parent self._committed = False self._callback = None self._items = {} def _my_api(self): raise NotImplementedError() def _my_keep(self): raise NotImplementedError() def _my_block_manager(self): raise NotImplementedError() def writable(self): raise NotImplementedError() def root_collection(self): raise NotImplementedError() def notify(self, event, collection, name, item): raise NotImplementedError() def stream_name(self): raise NotImplementedError() @must_be_writable @synchronized def find_or_create(self, path, create_type): """Recursively search the specified file path. May return either a `Collection` or `ArvadosFile`. If not found, will create a new item at the specified path based on `create_type`. Will create intermediate subcollections needed to contain the final item in the path. :create_type: One of `arvados.collection.FILE` or `arvados.collection.COLLECTION`. If the path is not found, and value of create_type is FILE then create and return a new ArvadosFile for the last path component. If COLLECTION, then create and return a new Collection for the last path component. """ pathcomponents = path.split("/", 1) if pathcomponents[0]: item = self._items.get(pathcomponents[0]) if len(pathcomponents) == 1: if item is None: # create new file if create_type == COLLECTION: item = Subcollection(self, pathcomponents[0]) else: item = ArvadosFile(self, pathcomponents[0]) self._items[pathcomponents[0]] = item self._committed = False self.notify(ADD, self, pathcomponents[0], item) return item else: if item is None: # create new collection item = Subcollection(self, pathcomponents[0]) self._items[pathcomponents[0]] = item self._committed = False self.notify(ADD, self, pathcomponents[0], item) if isinstance(item, RichCollectionBase): return item.find_or_create(pathcomponents[1], create_type) else: raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0]) else: return self @synchronized def find(self, path): """Recursively search the specified file path. May return either a Collection or ArvadosFile. Return None if not found. """ if not path: raise errors.ArgumentError("Parameter 'path' is empty.") pathcomponents = path.split("/", 1) item = self._items.get(pathcomponents[0]) if len(pathcomponents) == 1: return item else: if isinstance(item, RichCollectionBase): if pathcomponents[1]: return item.find(pathcomponents[1]) else: return item else: raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0]) @synchronized def mkdirs(self, path): """Recursive subcollection create. Like `os.makedirs()`. Will create intermediate subcollections needed to contain the leaf subcollection path. """ if self.find(path) != None: raise IOError(errno.EEXIST, "Directory or file exists", path) return self.find_or_create(path, COLLECTION) def open(self, path, mode="r"): """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 errors.ArgumentError("Bad mode '%s'" % mode) create = (mode != "r") if create and not self.writable(): raise IOError(errno.EROFS, "Collection is read only") if create: arvfile = self.find_or_create(path, FILE) else: arvfile = self.find(path) if arvfile is None: raise IOError(errno.ENOENT, "File not found", path) if not isinstance(arvfile, ArvadosFile): raise IOError(errno.EISDIR, "Is a directory", path) if mode[0] == "w": arvfile.truncate(0) name = os.path.basename(path) if mode == "r": return ArvadosFileReader(arvfile, num_retries=self.num_retries) else: return ArvadosFileWriter(arvfile, mode, num_retries=self.num_retries) def modified(self): """Determine if the collection has been modified since last commited.""" return not self.committed() @synchronized def committed(self): """Determine if the collection has been committed to the API server.""" if self._committed is False: return False for v in self._items.values(): if v.committed() is False: return False return True @synchronized def set_committed(self): """Recursively set committed flag to True.""" self._committed = True for k,v in self._items.items(): v.set_committed() @synchronized def __iter__(self): """Iterate over names of files and collections contained in this collection.""" return iter(self._items.keys()) @synchronized def __getitem__(self, k): """Get a file or collection that is directly contained by this collection. If you want to search a path, use `find()` instead. """ return self._items[k] @synchronized def __contains__(self, k): """Test if there is a file or collection a directly contained by this collection.""" return k in self._items @synchronized def __len__(self): """Get the number of items directly contained in this collection.""" return len(self._items) @must_be_writable @synchronized def __delitem__(self, p): """Delete an item by name which is directly contained by this collection.""" del self._items[p] self._committed = False self.notify(DEL, self, p, None) @synchronized def keys(self): """Get a list of names of files and collections directly contained in this collection.""" return self._items.keys() @synchronized def values(self): """Get a list of files and collection objects directly contained in this collection.""" return self._items.values() @synchronized def items(self): """Get a list of (name, object) tuples directly contained in this collection.""" return self._items.items() def exists(self, path): """Test if there is a file or collection at `path`.""" return self.find(path) is not None @must_be_writable @synchronized def remove(self, path, recursive=False): """Remove the file or subcollection (directory) at `path`. :recursive: Specify whether to remove non-empty subcollections (True), or raise an error (False). """ if not path: raise errors.ArgumentError("Parameter 'path' is empty.") pathcomponents = path.split("/", 1) item = self._items.get(pathcomponents[0]) if item is None: raise IOError(errno.ENOENT, "File not found", path) if len(pathcomponents) == 1: if isinstance(self._items[pathcomponents[0]], RichCollectionBase) and len(self._items[pathcomponents[0]]) > 0 and not recursive: raise IOError(errno.ENOTEMPTY, "Directory not empty", path) deleteditem = self._items[pathcomponents[0]] del self._items[pathcomponents[0]] self._committed = False self.notify(DEL, self, pathcomponents[0], deleteditem) else: item.remove(pathcomponents[1]) def _clonefrom(self, source): for k,v in source.items(): self._items[k] = v.clone(self, k) def clone(self): raise NotImplementedError() @must_be_writable @synchronized def add(self, source_obj, target_name, overwrite=False, reparent=False): """Copy or move a file or subcollection to this collection. :source_obj: An ArvadosFile, or Subcollection object :target_name: Destination item name. If the target name already exists and is a file, this will raise an error unless you specify `overwrite=True`. :overwrite: Whether to overwrite target file if it already exists. :reparent: If True, source_obj will be moved from its parent collection to this collection. If False, source_obj will be copied and the parent collection will be unmodified. """ if target_name in self and not overwrite: raise IOError(errno.EEXIST, "File already exists", target_name) modified_from = None if target_name in self: modified_from = self[target_name] # Actually make the move or copy. if reparent: source_obj._reparent(self, target_name) item = source_obj else: item = source_obj.clone(self, target_name) self._items[target_name] = item self._committed = False if modified_from: self.notify(MOD, self, target_name, (modified_from, item)) else: self.notify(ADD, self, target_name, item) def _get_src_target(self, source, target_path, source_collection, create_dest): if source_collection is None: source_collection = self # Find the object if isinstance(source, basestring): source_obj = source_collection.find(source) if source_obj is None: raise IOError(errno.ENOENT, "File not found", source) sourcecomponents = source.split("/") else: source_obj = source sourcecomponents = None # Find parent collection the target path targetcomponents = target_path.split("/") # Determine the name to use. target_name = targetcomponents[-1] if targetcomponents[-1] else sourcecomponents[-1] if not target_name: raise errors.ArgumentError("Target path is empty and source is an object. Cannot determine destination filename to use.") if create_dest: target_dir = self.find_or_create("/".join(targetcomponents[0:-1]), COLLECTION) else: if len(targetcomponents) > 1: target_dir = self.find("/".join(targetcomponents[0:-1])) else: target_dir = self if target_dir is None: raise IOError(errno.ENOENT, "Target directory not found", target_name) if target_name in target_dir and isinstance(self[target_name], RichCollectionBase) and sourcecomponents: target_dir = target_dir[target_name] target_name = sourcecomponents[-1] return (source_obj, target_dir, target_name) @must_be_writable @synchronized def copy(self, source, target_path, source_collection=None, overwrite=False): """Copy a file or subcollection to a new path in this collection. :source: A string with a path to source file or subcollection, or an actual ArvadosFile or Subcollection object. :target_path: Destination file or path. If the target path already exists and is a subcollection, the item will be placed inside the subcollection. If the target path already exists and is a file, this will raise an error unless you specify `overwrite=True`. :source_collection: Collection to copy `source_path` from (default `self`) :overwrite: Whether to overwrite target file if it already exists. """ source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, True) target_dir.add(source_obj, target_name, overwrite, False) @must_be_writable @synchronized def rename(self, source, target_path, source_collection=None, overwrite=False): """Move a file or subcollection from `source_collection` to a new path in this collection. :source: A string with a path to source file or subcollection. :target_path: Destination file or path. If the target path already exists and is a subcollection, the item will be placed inside the subcollection. If the target path already exists and is a file, this will raise an error unless you specify `overwrite=True`. :source_collection: Collection to copy `source_path` from (default `self`) :overwrite: Whether to overwrite target file if it already exists. """ source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, False) if not source_obj.writable(): raise IOError(errno.EROFS, "Source collection is read only", source) target_dir.add(source_obj, target_name, overwrite, True) def portable_manifest_text(self, stream_name="."): """Get the manifest text for this collection, sub collections and files. This method does not flush outstanding blocks to Keep. It will return a normalized manifest with access tokens stripped. :stream_name: Name to use for this stream (directory) """ return self._get_manifest_text(stream_name, True, True) @synchronized def manifest_text(self, stream_name=".", strip=False, normalize=False): """Get the manifest text for this collection, sub collections and files. This method will flush outstanding blocks to Keep. By default, it will not normalize an unmodified manifest or strip access tokens. :stream_name: Name to use for this stream (directory) :strip: If True, remove signing tokens from block locators if present. If False (default), 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 (default) and the collection is not modified, return the original manifest text even if it is not in normalized form. """ self._my_block_manager().commit_all() return self._get_manifest_text(stream_name, strip, normalize) @synchronized def _get_manifest_text(self, stream_name, strip, normalize, only_committed=False): """Get the manifest text for this collection, sub collections and files. :stream_name: Name to use for this stream (directory) :strip: If True, remove signing tokens from block locators if present. If False (default), 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 (default) and the collection is not modified, return the original manifest text even if it is not in normalized form. :only_committed: If True, only include blocks that were already committed to Keep. """ if not self.committed() or self._manifest_text is None or normalize: stream = {} buf = [] sorted_keys = sorted(self.keys()) for filename in [s for s in sorted_keys if isinstance(self[s], ArvadosFile)]: # Create a stream per file `k` arvfile = self[filename] filestream = [] for segment in arvfile.segments(): loc = segment.locator if arvfile.parent._my_block_manager().is_bufferblock(loc): if only_committed: continue loc = arvfile.parent._my_block_manager().get_bufferblock(loc).locator() if strip: loc = KeepLocator(loc).stripped() filestream.append(LocatorAndRange(loc, KeepLocator(loc).size, segment.segment_offset, segment.range_size)) stream[filename] = filestream if stream: buf.append(" ".join(normalize_stream(stream_name, stream)) + "\n") for dirname in [s for s in sorted_keys if isinstance(self[s], RichCollectionBase)]: buf.append(self[dirname].manifest_text(stream_name=os.path.join(stream_name, dirname), strip=strip, normalize=True)) return "".join(buf) else: if strip: return self.stripped_manifest() else: return self._manifest_text @synchronized def diff(self, end_collection, prefix=".", holding_collection=None): """Generate list of add/modify/delete actions. When given to `apply`, will change `self` to match `end_collection` """ changes = [] if holding_collection is None: holding_collection = Collection(api_client=self._my_api(), keep_client=self._my_keep()) for k in self: if k not in end_collection: changes.append((DEL, os.path.join(prefix, k), self[k].clone(holding_collection, ""))) for k in end_collection: if k in self: if isinstance(end_collection[k], Subcollection) and isinstance(self[k], Subcollection): changes.extend(self[k].diff(end_collection[k], os.path.join(prefix, k), holding_collection)) elif end_collection[k] != self[k]: changes.append((MOD, os.path.join(prefix, k), self[k].clone(holding_collection, ""), end_collection[k].clone(holding_collection, ""))) else: changes.append((TOK, os.path.join(prefix, k), self[k].clone(holding_collection, ""), end_collection[k].clone(holding_collection, ""))) else: changes.append((ADD, os.path.join(prefix, k), end_collection[k].clone(holding_collection, ""))) return changes @must_be_writable @synchronized def apply(self, changes): """Apply changes from `diff`. If a change conflicts with a local change, it will be saved to an alternate path indicating the conflict. """ if changes: self._committed = False for change in changes: event_type = change[0] path = change[1] initial = change[2] local = self.find(path) conflictpath = "%s~%s~conflict~" % (path, time.strftime("%Y%m%d-%H%M%S", time.gmtime())) if event_type == ADD: if local is None: # No local file at path, safe to copy over new file self.copy(initial, path) elif local is not None and local != initial: # There is already local file and it is different: # save change to conflict file. self.copy(initial, conflictpath) elif event_type == MOD or event_type == TOK: final = change[3] if local == initial: # Local matches the "initial" item so it has not # changed locally and is safe to update. if isinstance(local, ArvadosFile) and isinstance(final, ArvadosFile): # Replace contents of local file with new contents local.replace_contents(final) else: # Overwrite path with new item; this can happen if # path was a file and is now a collection or vice versa self.copy(final, path, overwrite=True) else: # Local is missing (presumably deleted) or local doesn't # match the "start" value, so save change to conflict file self.copy(final, conflictpath) elif event_type == DEL: if local == initial: # Local item matches "initial" value, so it is safe to remove. self.remove(path, recursive=True) # else, the file is modified or already removed, in either # case we don't want to try to remove it. def portable_data_hash(self): """Get the portable data hash for this collection's manifest.""" stripped = self.portable_manifest_text() return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped)) @synchronized def subscribe(self, callback): if self._callback is None: self._callback = callback else: raise errors.ArgumentError("A callback is already set on this collection.") @synchronized def unsubscribe(self): if self._callback is not None: self._callback = None @synchronized def notify(self, event, collection, name, item): if self._callback: self._callback(event, collection, name, item) self.root_collection().notify(event, collection, name, item) @synchronized def __eq__(self, other): if other is self: return True if not isinstance(other, RichCollectionBase): return False if len(self._items) != len(other): return False for k in self._items: if k not in other: return False if self._items[k] != other[k]: return False return True def __ne__(self, other): return not self.__eq__(other) @synchronized def flush(self): """Flush bufferblocks to Keep.""" for e in self.values(): e.flush() class Collection(RichCollectionBase): """Represents the root of an Arvados Collection. This class is threadsafe. The root collection object, all subcollections and files are protected by a single lock (i.e. each access locks the entire collection). Brief summary of useful methods: :To read an existing file: `c.open("myfile", "r")` :To write a new file: `c.open("myfile", "w")` :To determine if a file exists: `c.find("myfile") is not None` :To copy a file: `c.copy("source", "dest")` :To delete a file: `c.remove("myfile")` :To save to an existing collection record: `c.save()` :To save a new collection record: `c.save_new()` :To merge remote changes into this object: `c.update()` Must be associated with an API server Collection record (during initialization, or using `save_new`) to use `save` or `update` """ def __init__(self, manifest_locator_or_text=None, api_client=None, keep_client=None, num_retries=None, parent=None, apiconfig=None, block_manager=None, replication_desired=None): """Collection constructor. :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. :apiconfig: A dict containing keys for ARVADOS_API_HOST and ARVADOS_API_TOKEN. Prefer this over supplying your own api_client and keep_client (except in testing). Will use default config settings if not specified. :api_client: The API client object to use for requests. If not specified, create one using `apiconfig`. :keep_client: the Keep client to use for requests. If not specified, create one using `apiconfig`. :num_retries: the number of retries for API and Keep requests. :block_manager: the block manager to use. If not specified, create one. :replication_desired: How many copies should Arvados maintain. If None, API server default configuration applies. If not None, this value will also be used for determining the number of block copies being written. """ super(Collection, self).__init__(parent) self._api_client = api_client self._keep_client = keep_client self._block_manager = block_manager self.replication_desired = replication_desired if apiconfig: self._config = apiconfig else: self._config = config.settings() self.num_retries = num_retries if num_retries is not None else 0 self._manifest_locator = None self._manifest_text = None self._api_response = None self._past_versions = set() self.lock = threading.RLock() self.events = 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 is not a manifest or a collection UUID") try: self._populate() except (IOError, errors.SyntaxError) as e: raise errors.ArgumentError("Error processing manifest text: %s", e) def root_collection(self): return self def stream_name(self): return "." def writable(self): return True @synchronized def known_past_version(self, modified_at_and_portable_data_hash): return modified_at_and_portable_data_hash in self._past_versions @synchronized @retry_method def update(self, other=None, num_retries=None): """Merge the latest collection on the API server with the current collection.""" if other is None: if self._manifest_locator is None: raise errors.ArgumentError("`other` is None but collection does not have a manifest_locator uuid") response = self._my_api().collections().get(uuid=self._manifest_locator).execute(num_retries=num_retries) if (self.known_past_version((response.get("modified_at"), response.get("portable_data_hash"))) and response.get("portable_data_hash") != self.portable_data_hash()): # The record on the server is different from our current one, but we've seen it before, # so ignore it because it's already been merged. # However, if it's the same as our current record, proceed with the update, because we want to update # our tokens. return else: self._past_versions.add((response.get("modified_at"), response.get("portable_data_hash"))) other = CollectionReader(response["manifest_text"]) baseline = CollectionReader(self._manifest_text) self.apply(baseline.diff(other)) self._manifest_text = self.manifest_text() @synchronized def _my_api(self): if self._api_client is None: self._api_client = ThreadSafeApiCache(self._config) if self._keep_client is None: self._keep_client = self._api_client.keep return self._api_client @synchronized def _my_keep(self): if self._keep_client is None: if self._api_client is None: self._my_api() else: self._keep_client = KeepClient(api_client=self._api_client) return self._keep_client @synchronized def _my_block_manager(self): if self._block_manager is None: copies = (self.replication_desired or self._my_api()._rootDesc.get('defaultCollectionReplication', 2)) self._block_manager = _BlockManager(self._my_keep(), copies=copies) return self._block_manager def _remember_api_response(self, response): self._api_response = response self._past_versions.add((response.get("modified_at"), response.get("portable_data_hash"))) 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._remember_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'] # If not overriden via kwargs, we should try to load the # replication_desired from the API server if self.replication_desired is None: self.replication_desired = self._api_response.get('replication_desired', None) 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): 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 errors.NotFoundError( ("Failed to retrieve collection '{}' " + "from either API server ({}) or Keep ({})." ).format( self._manifest_locator, error_via_api, error_via_keep)) # populate self._baseline_manifest = self._manifest_text self._import_manifest(self._manifest_text) def _has_collection_uuid(self): return self._manifest_locator is not None and re.match(util.collection_uuid_pattern, self._manifest_locator) def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): """Support scoped auto-commit in a with: block.""" if exc_type is None: if self.writable() and self._has_collection_uuid(): self.save() self.stop_threads() def stop_threads(self): if self._block_manager is not None: self._block_manager.stop_threads() @synchronized def manifest_locator(self): """Get the manifest locator, if any. The manifest locator will be set when the collection is loaded from an API server record or the portable data hash of a manifest. The manifest locator will be None if the collection is newly created or was created directly from manifest text. The method `save_new()` will assign a manifest locator. """ return self._manifest_locator @synchronized def clone(self, new_parent=None, new_name=None, readonly=False, new_config=None): if new_config is None: new_config = self._config if readonly: newcollection = CollectionReader(parent=new_parent, apiconfig=new_config) else: newcollection = Collection(parent=new_parent, apiconfig=new_config) newcollection._clonefrom(self) return newcollection @synchronized def api_response(self): """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 find_or_create(self, path, create_type): """See `RichCollectionBase.find_or_create`""" if path == ".": return self else: return super(Collection, self).find_or_create(path[2:] if path.startswith("./") else path, create_type) def find(self, path): """See `RichCollectionBase.find`""" if path == ".": return self else: return super(Collection, self).find(path[2:] if path.startswith("./") else path) def remove(self, path, recursive=False): """See `RichCollectionBase.remove`""" if path == ".": raise errors.ArgumentError("Cannot remove '.'") else: return super(Collection, self).remove(path[2:] if path.startswith("./") else path, recursive) @must_be_writable @synchronized @retry_method def save(self, merge=True, num_retries=None): """Save collection to an existing collection record. Commit pending buffer blocks to Keep, merge with remote record (if merge=True, the default), and update the collection record. Returns the current manifest text. Will raise AssertionError if not associated with a collection record on the API server. If you want to save a manifest to Keep only, see `save_new()`. :merge: Update and merge remote changes before saving. Otherwise, any remote changes will be ignored and overwritten. :num_retries: Retry count on API calls (if None, use the collection default) """ if not self.committed(): if not self._has_collection_uuid(): raise AssertionError("Collection manifest_locator is not a collection uuid. Use save_new() for new collections.") self._my_block_manager().commit_all() if merge: self.update() text = self.manifest_text(strip=False) self._remember_api_response(self._my_api().collections().update( uuid=self._manifest_locator, body={'manifest_text': text} ).execute( num_retries=num_retries)) self._manifest_text = self._api_response["manifest_text"] self.set_committed() return self._manifest_text @must_be_writable @synchronized @retry_method def save_new(self, name=None, create_collection_record=True, owner_uuid=None, ensure_unique_name=False, num_retries=None): """Save collection to a new collection record. Commit pending buffer blocks to Keep and, when create_collection_record is True (default), create a new collection record. After creating a new collection record, this Collection object will be associated with the new record used by `save()`. Returns the current manifest text. :name: The collection name. :create_collection_record: If True, create a collection record on the API server. If False, only commit blocks to Keep and return the manifest text. :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. :num_retries: Retry count on API calls (if None, use the collection default) """ self._my_block_manager().commit_all() text = self.manifest_text(strip=False) if create_collection_record: if name is None: name = "New collection" ensure_unique_name = True body = {"manifest_text": text, "name": name, "replication_desired": self.replication_desired} if owner_uuid: body["owner_uuid"] = owner_uuid self._remember_api_response(self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries)) text = self._api_response["manifest_text"] self._manifest_locator = self._api_response["uuid"] self._manifest_text = text self.set_committed() return text @synchronized def _import_manifest(self, manifest_text): """Import a manifest into a `Collection`. :manifest_text: The manifest text to import from. """ if len(self) > 0: raise ArgumentError("Can only import manifest into an empty collection") STREAM_NAME = 0 BLOCKS = 1 SEGMENTS = 2 stream_name = None state = STREAM_NAME for token_and_separator in re.finditer(r'(\S+)(\s+|$)', manifest_text): tok = token_and_separator.group(1) sep = token_and_separator.group(2) if state == STREAM_NAME: # starting a new stream stream_name = tok.replace('\\040', ' ') blocks = [] segments = [] streamoffset = 0L state = BLOCKS self.find_or_create(stream_name, COLLECTION) continue if state == BLOCKS: block_locator = re.match(r'[0-9a-f]{32}\+(\d+)(\+\S+)*', tok) if block_locator: blocksize = long(block_locator.group(1)) blocks.append(Range(tok, streamoffset, blocksize, 0)) streamoffset += blocksize else: state = SEGMENTS if state == SEGMENTS: file_segment = re.search(r'^(\d+):(\d+):(\S+)', tok) if file_segment: pos = long(file_segment.group(1)) size = long(file_segment.group(2)) name = file_segment.group(3).replace('\\040', ' ') filepath = os.path.join(stream_name, name) afile = self.find_or_create(filepath, FILE) if isinstance(afile, ArvadosFile): afile.add_segment(blocks, pos, size) else: raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath) else: # error! raise errors.SyntaxError("Invalid manifest format, expected file segment but did not match format: '%s'" % tok) if sep == "\n": stream_name = None state = STREAM_NAME self.set_committed() @synchronized def notify(self, event, collection, name, item): if self._callback: self._callback(event, collection, name, item) class Subcollection(RichCollectionBase): """This is a subdirectory within a collection that doesn't have its own API server record. Subcollection locking falls under the umbrella lock of its root collection. """ def __init__(self, parent, name): super(Subcollection, self).__init__(parent) self.lock = self.root_collection().lock self._manifest_text = None self.name = name self.num_retries = parent.num_retries def root_collection(self): return self.parent.root_collection() def writable(self): return self.root_collection().writable() def _my_api(self): return self.root_collection()._my_api() def _my_keep(self): return self.root_collection()._my_keep() def _my_block_manager(self): return self.root_collection()._my_block_manager() def stream_name(self): return os.path.join(self.parent.stream_name(), self.name) @synchronized def clone(self, new_parent, new_name): c = Subcollection(new_parent, new_name) c._clonefrom(self) return c @must_be_writable @synchronized def _reparent(self, newparent, newname): self._committed = False self.flush() self.parent.remove(self.name, recursive=True) self.parent = newparent self.name = newname self.lock = self.parent.root_collection().lock class CollectionReader(Collection): """A read-only collection object. Initialize from an api collection record locator, a portable data hash of a manifest, or raw manifest text. See `Collection` constructor for detailed options. """ def __init__(self, manifest_locator_or_text, *args, **kwargs): self._in_init = True super(CollectionReader, self).__init__(manifest_locator_or_text, *args, **kwargs) self._in_init = False # Forego any locking since it should never change once initialized. self.lock = NoopLock() # Backwards compatability with old CollectionReader # all_streams() and all_files() self._streams = None def writable(self): return self._in_init def _populate_streams(orig_func): @functools.wraps(orig_func) def populate_streams_wrapper(self, *args, **kwargs): # Defer populating self._streams until needed since it creates a copy of the manifest. if self._streams is None: if self._manifest_text: self._streams = [sline.split() for sline in self._manifest_text.split("\n") if sline] else: self._streams = [] return orig_func(self, *args, **kwargs) return populate_streams_wrapper @_populate_streams def normalize(self): """Normalize the streams returned by `all_streams`. This method is kept for backwards compatability and only affects the behavior of `all_streams()` and `all_files()` """ # 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)] @_populate_streams def all_streams(self): return [StreamReader(s, self._my_keep(), num_retries=self.num_retries) for s in self._streams] @_populate_streams def all_files(self): for s in self.all_streams(): for f in s.all_files(): yield f