X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b0e6c00576257cef24cfd0599073f58904a2b85c..49bfee2a221bb050732935c240b981b7becd9aff:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index 599e91dd45..cce7d75685 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -1,3 +1,12 @@ +# 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 @@ -11,20 +20,22 @@ 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 +62,7 @@ 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 +93,8 @@ 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 +193,7 @@ 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 +229,11 @@ 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 +273,7 @@ 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( @@ -346,11 +363,12 @@ 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() @@ -372,8 +390,18 @@ 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', @@ -418,7 +446,7 @@ 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: @@ -544,7 +572,7 @@ class RichCollectionBase(CollectionBase): else: item = ArvadosFile(self, pathcomponents[0]) self._items[pathcomponents[0]] = item - self._committed = False + self.set_committed(False) self.notify(ADD, self, pathcomponents[0], item) return item else: @@ -552,7 +580,7 @@ class RichCollectionBase(CollectionBase): # create new collection item = Subcollection(self, pathcomponents[0]) self._items[pathcomponents[0]] = item - self._committed = False + self.set_committed(False) self.notify(ADD, self, pathcomponents[0], item) if isinstance(item, RichCollectionBase): return item.find_or_create(pathcomponents[1], create_type) @@ -612,7 +640,12 @@ 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+": @@ -624,33 +657,28 @@ 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", path) if not isinstance(arvfile, ArvadosFile): raise IOError(errno.EISDIR, "Is a directory", path) - if mode[0] == "w": + 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) + return fclass(arvfile, mode=mode, num_retries=self.num_retries) def modified(self): """Determine if the collection has been modified since last commited.""" @@ -659,25 +687,31 @@ class RichCollectionBase(CollectionBase): @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 + return self._committed @synchronized - def set_committed(self): - """Recursively set committed flag to True.""" - self._committed = True - for k,v in self._items.items(): - v.set_committed() + 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): @@ -703,7 +737,7 @@ class RichCollectionBase(CollectionBase): def __delitem__(self, p): """Delete an item by name which is directly contained by this collection.""" del self._items[p] - self._committed = False + self.set_committed(False) self.notify(DEL, self, p, None) @synchronized @@ -714,12 +748,12 @@ 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`.""" @@ -746,13 +780,13 @@ class RichCollectionBase(CollectionBase): raise IOError(errno.ENOTEMPTY, "Directory not empty", path) deleteditem = self._items[pathcomponents[0]] del self._items[pathcomponents[0]] - self._committed = False + 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(): + for k,v in listitems(source): self._items[k] = v.clone(self, k) def clone(self): @@ -795,7 +829,7 @@ class RichCollectionBase(CollectionBase): item = source_obj.clone(self, target_name) self._items[target_name] = item - self._committed = False + self.set_committed(False) if modified_from: self.notify(MOD, self, target_name, (modified_from, item)) @@ -905,7 +939,8 @@ class RichCollectionBase(CollectionBase): return self._get_manifest_text(stream_name, True, True) @synchronized - def manifest_text(self, stream_name=".", strip=False, normalize=False): + 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 @@ -924,10 +959,15 @@ 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, only_committed=False): @@ -973,10 +1013,7 @@ 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)]: - if only_committed: - buf.append(self[dirname]._get_manifest_text(stream_name=os.path.join(stream_name, dirname), strip=strip, normalize=True, only_committed=only_committed)) - else: - 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: @@ -1019,7 +1056,7 @@ class RichCollectionBase(CollectionBase): """ if changes: - self._committed = False + self.set_committed(False) for change in changes: event_type = change[0] path = change[1] @@ -1060,8 +1097,13 @@ 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): @@ -1102,7 +1144,7 @@ class RichCollectionBase(CollectionBase): @synchronized def flush(self): """Flush bufferblocks to Keep.""" - for e in self.values(): + for e in listvalues(self): e.flush() @@ -1157,8 +1199,9 @@ class Collection(RichCollectionBase): """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. @@ -1200,6 +1243,7 @@ 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() @@ -1207,11 +1251,11 @@ class Collection(RichCollectionBase): 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( @@ -1296,66 +1340,27 @@ 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._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 + 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 @@ -1431,7 +1436,7 @@ class Collection(RichCollectionBase): @must_be_writable @synchronized @retry_method - def save(self, merge=True, num_retries=None): + def save(self, storage_classes=None, merge=True, num_retries=None): """Save collection to an existing collection record. Commit pending buffer blocks to Keep, merge with remote record (if @@ -1460,13 +1465,18 @@ class Collection(RichCollectionBase): self.update() text = self.manifest_text(strip=False) + body={'manifest_text': text} + if storage_classes: + body["storage_classes_desired"] = storage_classes + self._remember_api_response(self._my_api().collections().update( uuid=self._manifest_locator, - body={'manifest_text': text} + body=body ).execute( num_retries=num_retries)) self._manifest_text = self._api_response["manifest_text"] - self.set_committed() + self._portable_data_hash = self._api_response["portable_data_hash"] + self.set_committed(True) return self._manifest_text @@ -1477,6 +1487,7 @@ class Collection(RichCollectionBase): def save_new(self, name=None, create_collection_record=True, owner_uuid=None, + storage_classes=None, ensure_unique_name=False, num_retries=None): """Save collection to a new collection record. @@ -1519,17 +1530,24 @@ class Collection(RichCollectionBase): "replication_desired": self.replication_desired} if owner_uuid: body["owner_uuid"] = owner_uuid + if storage_classes: + body["storage_classes_desired"] = storage_classes 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_committed() + self.set_committed(True) return text + _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): """Import a manifest into a `Collection`. @@ -1548,7 +1566,7 @@ 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) @@ -1557,25 +1575,25 @@ 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) @@ -1591,7 +1609,7 @@ class Collection(RichCollectionBase): stream_name = None state = STREAM_NAME - self.set_committed() + self.set_committed(True) @synchronized def notify(self, event, collection, name, item): @@ -1641,7 +1659,7 @@ class Subcollection(RichCollectionBase): @must_be_writable @synchronized def _reparent(self, newparent, newname): - self._committed = False + self.set_committed(False) self.flush() self.parent.remove(self.name, recursive=True) self.parent = newparent @@ -1652,9 +1670,8 @@ class Subcollection(RichCollectionBase): 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):