X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/6eb3d1fb8fe71623fa63da46c250184cf2e4fbb8..e2cc6c1935565ee965f38501a4974e9d0e6b29e5:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index 30828732d8..e38a6bd475 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -1,9 +1,20 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + +from __future__ import absolute_import +from future.utils import listitems, listvalues, viewkeys +from builtins import str +from past.builtins import basestring +from builtins import object import functools import logging import os import re import errno import hashlib +import datetime +import ciso8601 import time import threading @@ -11,20 +22,22 @@ 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 .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 +import arvados.config as config +import arvados.errors as errors +import arvados.util +import arvados.events as events from arvados.retry import retry_method _logger = logging.getLogger('arvados.collection') class CollectionBase(object): + """Abstract base class for Collection classes.""" + def __enter__(self): return self @@ -51,7 +64,7 @@ class CollectionBase(object): if fields: clean_fields = fields[:1] + [ (re.sub(r'\+[^\d][^\+]*', '', x) - if re.match(util.keep_locator_pattern, x) + if re.match(arvados.util.keep_locator_pattern, x) else x) for x in fields[1:]] clean += [' '.join(clean_fields), "\n"] @@ -82,6 +95,8 @@ class _WriterFile(_FileLikeObjectBase): class CollectionWriter(CollectionBase): + """Deprecated, use Collection instead.""" + def __init__(self, api_client=None, num_retries=0, replication=None): """Instantiate a CollectionWriter. @@ -180,7 +195,7 @@ class CollectionWriter(CollectionBase): def _work_trees(self): path, stream_name, max_manifest_depth = self._queued_trees[0] - d = util.listdir_recursive( + d = arvados.util.listdir_recursive( path, max_depth = (None if max_manifest_depth == 0 else 0)) if d: self._queue_dirents(stream_name, d) @@ -216,7 +231,11 @@ class CollectionWriter(CollectionBase): self.do_queued_work() def write(self, newdata): - if hasattr(newdata, '__iter__'): + if isinstance(newdata, bytes): + pass + elif isinstance(newdata, str): + newdata = newdata.encode() + elif hasattr(newdata, '__iter__'): for s in newdata: self.write(s) return @@ -256,7 +275,7 @@ class CollectionWriter(CollectionBase): return self._last_open def flush_data(self): - data_buffer = ''.join(self._data_buffer) + data_buffer = b''.join(self._data_buffer) if data_buffer: self._current_stream_locators.append( self._my_keep().put( @@ -307,7 +326,8 @@ class CollectionWriter(CollectionBase): def set_current_stream_name(self, newstreamname): if re.search(r'[\t\n]', newstreamname): raise errors.AssertionError( - "Manifest stream names cannot contain whitespace") + "Manifest stream names cannot contain whitespace: '%s'" % + (newstreamname)) self._current_stream_name = '.' if newstreamname=='' else newstreamname def current_stream_name(self): @@ -345,11 +365,12 @@ class CollectionWriter(CollectionBase): sending manifest_text() to the API server's "create collection" endpoint. """ - return self._my_keep().put(self.manifest_text(), copies=self.replication) + return self._my_keep().put(self.manifest_text().encode(), + copies=self.replication) def portable_data_hash(self): - stripped = self.stripped_manifest() - return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped)) + stripped = self.stripped_manifest().encode() + return '{}+{}'.format(hashlib.md5(stripped).hexdigest(), len(stripped)) def manifest_text(self): self.finish_current_stream() @@ -371,8 +392,18 @@ class CollectionWriter(CollectionBase): ret += locators return ret + def save_new(self, name=None): + return self._api_client.collections().create( + ensure_unique_name=True, + body={ + 'name': name, + 'manifest_text': self.manifest_text(), + }).execute(num_retries=self.num_retries) + class ResumableCollectionWriter(CollectionWriter): + """Deprecated, use Collection instead.""" + STATE_PROPS = ['_current_stream_files', '_current_stream_length', '_current_stream_locators', '_current_stream_name', '_current_file_name', '_current_file_pos', '_close_file', @@ -417,7 +448,7 @@ class ResumableCollectionWriter(CollectionWriter): return writer def check_dependencies(self): - for path, orig_stat in self._dependencies.items(): + for path, orig_stat in listitems(self._dependencies): if not S_ISREG(orig_stat[ST_MODE]): raise errors.StaleWriterStateError("{} not file".format(path)) try: @@ -474,6 +505,7 @@ class ResumableCollectionWriter(CollectionWriter): ADD = "add" DEL = "del" MOD = "mod" +TOK = "tok" FILE = "file" COLLECTION = "collection" @@ -487,7 +519,8 @@ class RichCollectionBase(CollectionBase): def __init__(self, parent=None): self.parent = parent - self._modified = True + self._committed = False + self._callback = None self._items = {} def _my_api(self): @@ -537,24 +570,24 @@ class RichCollectionBase(CollectionBase): if item is None: # create new file if create_type == COLLECTION: - item = Subcollection(self) + item = Subcollection(self, pathcomponents[0]) else: - item = ArvadosFile(self) + item = ArvadosFile(self, pathcomponents[0]) self._items[pathcomponents[0]] = item - self._modified = True + self.set_committed(False) self.notify(ADD, self, pathcomponents[0], item) return item else: if item is None: # create new collection - item = Subcollection(self) + item = Subcollection(self, pathcomponents[0]) self._items[pathcomponents[0]] = item - self._modified = True + self.set_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, "Interior path components must be subcollection")) + raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0]) else: return self @@ -562,16 +595,23 @@ class RichCollectionBase(CollectionBase): def find(self, path): """Recursively search the specified file path. - May return either a Collection or ArvadosFile. Return None if not + May return either a Collection or ArvadosFile. Return None if not found. + If path is invalid (ex: starts with '/'), an IOError exception will be + raised. """ if not path: - raise errors.ArgumentError("Parameter 'path' must not be empty.") + raise errors.ArgumentError("Parameter 'path' is empty.") pathcomponents = path.split("/", 1) + if pathcomponents[0] == '': + raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0]) + item = self._items.get(pathcomponents[0]) - if len(pathcomponents) == 1: + if item is None: + return None + elif len(pathcomponents) == 1: return item else: if isinstance(item, RichCollectionBase): @@ -580,15 +620,20 @@ class RichCollectionBase(CollectionBase): else: return item else: - raise IOError((errno.ENOTDIR, "Interior path components must be subcollection")) + raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0]) - def mkdirs(path): + @synchronized + def mkdirs(self, path): """Recursive subcollection create. - Like `os.mkdirs()`. Will create intermediate subcollections needed to - contain the leaf subcollection path. + 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"): @@ -597,7 +642,12 @@ class RichCollectionBase(CollectionBase): :path: path to a file in the collection :mode: - one of "r", "r+", "w", "w+", "a", "a+" + a string consisting of "r", "w", or "a", optionally followed + by "b" or "t", optionally followed by "+". + :"b": + binary mode: write() accepts bytes, read() returns bytes. + :"t": + text mode (default): write() accepts strings, read() returns strings. :"r": opens for reading :"r+": @@ -609,55 +659,61 @@ class RichCollectionBase(CollectionBase): 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 not re.search(r'^[rwa][bt]?\+?$', mode): + raise errors.ArgumentError("Invalid mode {!r}".format(mode)) - if create: - arvfile = self.find_or_create(path, FILE) - else: + if mode[0] == 'r' and '+' not in mode: + fclass = ArvadosFileReader arvfile = self.find(path) + elif not self.writable(): + raise IOError(errno.EROFS, "Collection is read only") + else: + fclass = ArvadosFileWriter + arvfile = self.find_or_create(path, FILE) if arvfile is None: - raise IOError((errno.ENOENT, "File not found")) + raise IOError(errno.ENOENT, "File not found", path) if not isinstance(arvfile, ArvadosFile): - raise IOError((errno.EISDIR, "Path must refer to a file.")) + raise IOError(errno.EISDIR, "Is a directory", path) - if mode[0] == "w": + if mode[0] == 'w': arvfile.truncate(0) - name = os.path.basename(path) + return fclass(arvfile, mode=mode, num_retries=self.num_retries) - if mode == "r": - return ArvadosFileReader(arvfile, name, mode, num_retries=self.num_retries) - else: - return ArvadosFileWriter(arvfile, name, 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 modified(self): - """Test if the collection (or any subcollection or file) has been modified.""" - if self._modified: - return True - for k,v in self._items.items(): - if v.modified(): - return True - return False + def committed(self): + """Determine if the collection has been committed to the API server.""" + return self._committed @synchronized - def set_unmodified(self): - """Recursively clear modified flag.""" - self._modified = False - for k,v in self._items.items(): - v.set_unmodified() + def set_committed(self, value=True): + """Recursively set committed flag. + + If value is True, set committed to be True for this and all children. + + If value is False, set committed to be False for this and all parents. + """ + if value == self._committed: + return + if value: + for k,v in listitems(self._items): + v.set_committed(True) + self._committed = True + else: + self._committed = False + if self.parent is not None: + self.parent.set_committed(False) @synchronized def __iter__(self): """Iterate over names of files and collections contained in this collection.""" - return iter(self._items.keys()) + return iter(viewkeys(self._items)) @synchronized def __getitem__(self, k): @@ -683,7 +739,7 @@ class RichCollectionBase(CollectionBase): def __delitem__(self, p): """Delete an item by name which is directly contained by this collection.""" del self._items[p] - self._modified = True + self.set_committed(False) self.notify(DEL, self, p, None) @synchronized @@ -694,12 +750,12 @@ class RichCollectionBase(CollectionBase): @synchronized def values(self): """Get a list of files and collection objects directly contained in this collection.""" - return self._items.values() + return listvalues(self._items) @synchronized def items(self): """Get a list of (name, object) tuples directly contained in this collection.""" - return self._items.items() + return listitems(self._items) def exists(self, path): """Test if there is a file or collection at `path`.""" @@ -715,33 +771,33 @@ class RichCollectionBase(CollectionBase): """ if not path: - raise errors.ArgumentError("Parameter 'path' must not be empty.") + 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")) + 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, "Subcollection not empty")) + raise IOError(errno.ENOTEMPTY, "Directory not empty", path) deleteditem = self._items[pathcomponents[0]] del self._items[pathcomponents[0]] - self._modified = True + self.set_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) + for k,v in listitems(source): + 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): - """Copy a file or subcollection to this collection. + 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 @@ -753,24 +809,74 @@ class RichCollectionBase(CollectionBase): :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")) + 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 copy. - dup = source_obj.clone(self) - self._items[target_name] = dup - self._modified = True + # 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.set_committed(False) if modified_from: - self.notify(MOD, self, target_name, (modified_from, dup)) + 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: - self.notify(ADD, self, target_name, dup) + 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(target_dir[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 @@ -792,35 +898,35 @@ class RichCollectionBase(CollectionBase): :overwrite: Whether to overwrite target file if it already exists. """ - if source_collection is None: - source_collection = self - # Find the object to copy - if isinstance(source, basestring): - source_obj = source_collection.find(source) - if source_obj is None: - raise IOError((errno.ENOENT, "File not found")) - sourcecomponents = source.split("/") - else: - source_obj = source - sourcecomponents = None + 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) - # Find parent collection the target path - targetcomponents = target_path.split("/") + @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. - # Determine the name to use. - target_name = targetcomponents[-1] if targetcomponents[-1] else (sourcecomponents[-1] if sourcecomponents else None) + :source: + A string with a path to source file or subcollection. - if not target_name: - raise errors.ArgumentError("Target path is empty and source is an object. Cannot determine destination filename to use.") + :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`. - target_dir = self.find_or_create("/".join(targetcomponents[0:-1]), COLLECTION) + :source_collection: + Collection to copy `source_path` from (default `self`) - if target_name in target_dir and isinstance(self[target_name], RichCollectionBase) and sourcecomponents: - target_dir = target_dir[target_name] - target_name = sourcecomponents[-1] + :overwrite: + Whether to overwrite target file if it already exists. + """ - target_dir.add(source_obj, target_name, overwrite) + 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. @@ -834,7 +940,9 @@ class RichCollectionBase(CollectionBase): """ return self._get_manifest_text(stream_name, True, True) - def manifest_text(self, stream_name=".", strip=False, normalize=False): + @synchronized + def manifest_text(self, stream_name=".", strip=False, normalize=False, + only_committed=False): """Get the manifest text for this collection, sub collections and files. This method will flush outstanding blocks to Keep. By default, it will @@ -853,13 +961,18 @@ class RichCollectionBase(CollectionBase): is not modified, return the original manifest text even if it is not in normalized form. + :only_committed: + If True, don't commit pending blocks. + """ - self._my_block_manager().commit_all() - return self._get_manifest_text(stream_name, strip, normalize) + if not only_committed: + self._my_block_manager().commit_all() + return self._get_manifest_text(stream_name, strip, normalize, + only_committed=only_committed) @synchronized - def _get_manifest_text(self, stream_name, strip, normalize): + 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: @@ -875,9 +988,12 @@ class RichCollectionBase(CollectionBase): 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 self.modified() or self._manifest_text is None or normalize: + if not self.committed() or self._manifest_text is None or normalize: stream = {} buf = [] sorted_keys = sorted(self.keys()) @@ -888,6 +1004,8 @@ class RichCollectionBase(CollectionBase): 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() @@ -897,7 +1015,7 @@ class RichCollectionBase(CollectionBase): 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)) + buf.append(self[dirname].manifest_text(stream_name=os.path.join(stream_name, dirname), strip=strip, normalize=True, only_committed=only_committed)) return "".join(buf) else: if strip: @@ -917,15 +1035,17 @@ class RichCollectionBase(CollectionBase): 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))) + 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))) + 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))) + changes.append((ADD, os.path.join(prefix, k), end_collection[k].clone(holding_collection, ""))) return changes @must_be_writable @@ -937,12 +1057,14 @@ class RichCollectionBase(CollectionBase): alternate path indicating the conflict. """ + if changes: + self.set_committed(False) for change in changes: event_type = change[0] path = change[1] initial = change[2] local = self.find(path) - conflictpath = "%s~conflict-%s~" % (path, time.strftime("%Y-%m-%d-%H:%M:%S", + conflictpath = "%s~%s~conflict~" % (path, time.strftime("%Y%m%d-%H%M%S", time.gmtime())) if event_type == ADD: if local is None: @@ -952,7 +1074,7 @@ class RichCollectionBase(CollectionBase): # There is already local file and it is different: # save change to conflict file. self.copy(initial, conflictpath) - elif event_type == MOD: + elif event_type == MOD or event_type == TOK: final = change[3] if local == initial: # Local matches the "initial" item so it has not @@ -977,8 +1099,31 @@ class RichCollectionBase(CollectionBase): 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)) + if self._manifest_locator and self.committed(): + # If the collection is already saved on the API server, and it's committed + # then return API server's PDH response. + return self._portable_data_hash + else: + stripped = self.portable_manifest_text().encode() + return '{}+{}'.format(hashlib.md5(stripped).hexdigest(), 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): @@ -998,6 +1143,12 @@ class RichCollectionBase(CollectionBase): def __ne__(self, other): return not self.__eq__(other) + @synchronized + def flush(self): + """Flush bufferblocks to Keep.""" + for e in listvalues(self): + e.flush() + class Collection(RichCollectionBase): """Represents the root of an Arvados Collection. @@ -1044,32 +1195,47 @@ class Collection(RichCollectionBase): num_retries=None, parent=None, apiconfig=None, - block_manager=None): + block_manager=None, + replication_desired=None, + put_threads=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). + An Arvados collection UUID, portable data hash, raw manifest + text, or (if creating an empty collection) None. + :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 + self.put_threads = put_threads if apiconfig: self._config = apiconfig @@ -1079,22 +1245,23 @@ class Collection(RichCollectionBase): self.num_retries = num_retries if num_retries is not None else 0 self._manifest_locator = None self._manifest_text = None + self._portable_data_hash = None self._api_response = None + self._past_versions = set() self.lock = threading.RLock() - self.callbacks = [] self.events = None if manifest_locator_or_text: - if re.match(util.keep_locator_pattern, manifest_locator_or_text): + if re.match(arvados.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): + elif re.match(arvados.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): + elif re.match(arvados.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") + "Argument to CollectionReader is not a manifest or a collection UUID") try: self._populate() @@ -1104,12 +1271,28 @@ class Collection(RichCollectionBase): def root_collection(self): return self + def get_properties(self): + if self._api_response and self._api_response["properties"]: + return self._api_response["properties"] + else: + return {} + + def get_trash_at(self): + if self._api_response and self._api_response["trash_at"]: + return ciso8601.parse_datetime(self._api_response["trash_at"]) + else: + return None + 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): @@ -1119,15 +1302,26 @@ class Collection(RichCollectionBase): 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) - self._keep_client = self._api_client.keep + if self._keep_client is None: + self._keep_client = self._api_client.keep return self._api_client @synchronized @@ -1142,9 +1336,16 @@ class Collection(RichCollectionBase): @synchronized def _my_block_manager(self): if self._block_manager is None: - self._block_manager = _BlockManager(self._my_keep()) + copies = (self.replication_desired or + self._my_api()._rootDesc.get('defaultCollectionReplication', + 2)) + self._block_manager = _BlockManager(self._my_keep(), copies=copies, put_threads=self.put_threads) 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 @@ -1153,71 +1354,39 @@ class Collection(RichCollectionBase): # 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 + 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'] + self._portable_data_hash = self._api_response['portable_data_hash'] + # 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) 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 + if self._manifest_locator is None: + return + else: + self._populate_from_api_server() 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) + return self._manifest_locator is not None and re.match(arvados.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 not None: + 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() @@ -1236,7 +1405,7 @@ class Collection(RichCollectionBase): return self._manifest_locator @synchronized - def clone(self, new_parent=None, readonly=False, new_config=None): + 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: @@ -1281,17 +1450,34 @@ class Collection(RichCollectionBase): @must_be_writable @synchronized @retry_method - def save(self, merge=True, num_retries=None): + def save(self, + properties=None, + storage_classes=None, + trash_at=None, + 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 + 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()`. + :properties: + Additional properties of collection. This value will replace any existing + properties of collection. + + :storage_classes: + Specify desirable storage classes to be used when writing data to Keep. + + :trash_at: + A collection is *expiring* when it has a *trash_at* time in the future. + An expiring collection can be accessed as normal, + but is scheduled to be trashed automatically at the *trash_at* time. + :merge: Update and merge remote changes before saving. Otherwise, any remote changes will be ignored and overwritten. @@ -1300,9 +1486,27 @@ class Collection(RichCollectionBase): Retry count on API calls (if None, use the collection default) """ - if self.modified(): + if properties and type(properties) is not dict: + raise errors.ArgumentError("properties must be dictionary type.") + + if storage_classes and type(storage_classes) is not list: + raise errors.ArgumentError("storage_classes must be list type.") + + if trash_at and type(trash_at) is not datetime.datetime: + raise errors.ArgumentError("trash_at must be datetime type.") + + body={} + if properties: + body["properties"] = properties + if storage_classes: + body["storage_classes_desired"] = storage_classes + if trash_at: + t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ") + body["trash_at"] = t + + if not self.committed(): if not self._has_collection_uuid(): - raise AssertionError("Collection manifest_locator must be a collection uuid. Use save_new() for new collections.") + raise AssertionError("Collection manifest_locator is not a collection uuid. Use save_new() for new collections.") self._my_block_manager().commit_all() @@ -1310,13 +1514,20 @@ class Collection(RichCollectionBase): self.update() text = self.manifest_text(strip=False) - self._api_response = self._my_api().collections().update( + body['manifest_text'] = text + + self._remember_api_response(self._my_api().collections().update( uuid=self._manifest_locator, - body={'manifest_text': text} - ).execute( - num_retries=num_retries) + body=body + ).execute(num_retries=num_retries)) self._manifest_text = self._api_response["manifest_text"] - self.set_unmodified() + self._portable_data_hash = self._api_response["portable_data_hash"] + self.set_committed(True) + elif body: + self._remember_api_response(self._my_api().collections().update( + uuid=self._manifest_locator, + body=body + ).execute(num_retries=num_retries)) return self._manifest_text @@ -1327,6 +1538,9 @@ class Collection(RichCollectionBase): def save_new(self, name=None, create_collection_record=True, owner_uuid=None, + properties=None, + storage_classes=None, + trash_at=None, ensure_unique_name=False, num_retries=None): """Save collection to a new collection record. @@ -1334,7 +1548,7 @@ class Collection(RichCollectionBase): 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. + the new record used by `save()`. Returns the current manifest text. :name: The collection name. @@ -1347,6 +1561,18 @@ class Collection(RichCollectionBase): the user, or project uuid that will own this collection. If None, defaults to the current user. + :properties: + Additional properties of collection. This value will replace any existing + properties of collection. + + :storage_classes: + Specify desirable storage classes to be used when writing data to Keep. + + :trash_at: + A collection is *expiring* when it has a *trash_at* time in the future. + An expiring collection can be accessed as normal, + but is scheduled to be trashed automatically at the *trash_at* time. + :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 @@ -1356,40 +1582,50 @@ class Collection(RichCollectionBase): Retry count on API calls (if None, use the collection default) """ + if properties and type(properties) is not dict: + raise errors.ArgumentError("properties must be dictionary type.") + + if storage_classes and type(storage_classes) is not list: + raise errors.ArgumentError("storage_classes must be list type.") + + if trash_at and type(trash_at) is not datetime.datetime: + raise errors.ArgumentError("trash_at must be datetime type.") + self._my_block_manager().commit_all() text = self.manifest_text(strip=False) if create_collection_record: if name is None: - name = "Collection created %s" % (time.strftime("%Y-%m-%d %H:%M:%S %Z", time.localtime())) + name = "New collection" + ensure_unique_name = True body = {"manifest_text": text, - "name": name} + "name": name, + "replication_desired": self.replication_desired} 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=num_retries) + if properties: + body["properties"] = properties + if storage_classes: + body["storage_classes_desired"] = storage_classes + if trash_at: + t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ") + body["trash_at"] = t + + 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._portable_data_hash = self._api_response["portable_data_hash"] self._manifest_text = text - self.set_unmodified() + self.set_committed(True) return text - @synchronized - def subscribe(self, callback): - self.callbacks.append(callback) - - @synchronized - def unsubscribe(self, callback): - self.callbacks.remove(callback) - - @synchronized - def notify(self, event, collection, name, item): - for c in self.callbacks: - c(event, collection, name, item) + _token_re = re.compile(r'(\S+)(\s+|$)') + _block_re = re.compile(r'[0-9a-f]{32}\+(\d+)(\+\S+)*') + _segment_re = re.compile(r'(\d+):(\d+):(\S+)') @synchronized def _import_manifest(self, manifest_text): @@ -1409,7 +1645,7 @@ class Collection(RichCollectionBase): stream_name = None state = STREAM_NAME - for token_and_separator in re.finditer(r'(\S+)(\s+|$)', manifest_text): + for token_and_separator in self._token_re.finditer(manifest_text): tok = token_and_separator.group(1) sep = token_and_separator.group(2) @@ -1418,24 +1654,25 @@ class Collection(RichCollectionBase): stream_name = tok.replace('\\040', ' ') blocks = [] segments = [] - streamoffset = 0L + streamoffset = 0 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) + block_locator = self._block_re.match(tok) if block_locator: - blocksize = long(block_locator.group(1)) + blocksize = int(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) + file_segment = self._segment_re.match(tok) if file_segment: - pos = long(file_segment.group(1)) - size = long(file_segment.group(2)) + pos = int(file_segment.group(1)) + size = int(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) @@ -1445,27 +1682,34 @@ class Collection(RichCollectionBase): raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath) else: # error! - raise errors.SyntaxError("Invalid manifest format") + 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_unmodified() + self.set_committed(True) + + @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. - It falls under the umbrella of the root collection. + Subcollection locking falls under the umbrella lock of its root collection. """ - def __init__(self, parent): + 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() @@ -1482,28 +1726,31 @@ class Subcollection(RichCollectionBase): def _my_block_manager(self): return self.root_collection()._my_block_manager() - def notify(self, event, collection, name, item): - return self.root_collection().notify(event, collection, name, item) - def stream_name(self): - for k, v in self.parent.items(): - if v is self: - return os.path.join(self.parent.stream_name(), k) - return '.' + return os.path.join(self.parent.stream_name(), self.name) @synchronized - def clone(self, new_parent): - c = Subcollection(new_parent) + 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.set_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. + Initialize from a collection UUID or portable data hash, or raw + manifest text. See `Collection` constructor for detailed options. """ def __init__(self, manifest_locator_or_text, *args, **kwargs):