X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b02e3cf1ccf3c9f50252c416b84932377270ddab..0eb72b526bf8bbb011551ecf019f604e17a534f1:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index 56d8b23933..7f78365fb5 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 @@ -11,15 +20,15 @@ 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') @@ -51,7 +60,7 @@ 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"] @@ -180,7 +189,7 @@ 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 +225,11 @@ 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 +269,7 @@ 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 +320,8 @@ 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 +359,12 @@ 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() @@ -417,7 +432,7 @@ 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: @@ -543,7 +558,7 @@ 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: @@ -551,12 +566,12 @@ 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) else: - raise IOError(errno.ENOTDIR, "Not a directory: '%s'" % pathcomponents[0]) + raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0]) else: return self @@ -564,16 +579,23 @@ 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' 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): @@ -582,7 +604,7 @@ class RichCollectionBase(CollectionBase): else: return item else: - raise IOError(errno.ENOTDIR, "Is not a directory: %s" % pathcomponents[0]) + raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0]) @synchronized def mkdirs(self, path): @@ -594,7 +616,7 @@ class RichCollectionBase(CollectionBase): """ if self.find(path) != None: - raise IOError(errno.EEXIST, "Directory or file exists: '%s'" % path) + raise IOError(errno.EEXIST, "Directory or file exists", path) return self.find_or_create(path, COLLECTION) @@ -604,7 +626,12 @@ 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+": @@ -616,33 +643,28 @@ 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") + raise IOError(errno.ENOENT, "File not found", path) if not isinstance(arvfile, ArvadosFile): - raise IOError(errno.EISDIR, "Is a directory: %s" % path) + 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.""" @@ -651,25 +673,31 @@ 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): @@ -695,7 +723,7 @@ 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 @@ -706,12 +734,12 @@ 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`.""" @@ -732,19 +760,19 @@ class RichCollectionBase(CollectionBase): 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._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): @@ -773,7 +801,7 @@ class RichCollectionBase(CollectionBase): """ 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: @@ -787,7 +815,7 @@ 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)) @@ -802,7 +830,7 @@ class RichCollectionBase(CollectionBase): if isinstance(source, basestring): source_obj = source_collection.find(source) if source_obj is None: - raise IOError(errno.ENOENT, "File not found") + raise IOError(errno.ENOENT, "File not found", source) sourcecomponents = source.split("/") else: source_obj = source @@ -826,9 +854,9 @@ class RichCollectionBase(CollectionBase): target_dir = self if target_dir is None: - raise IOError(errno.ENOENT, "Target directory not found.") + raise IOError(errno.ENOENT, "Target directory not found", target_name) - if target_name in target_dir and isinstance(self[target_name], RichCollectionBase) and sourcecomponents: + 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] @@ -881,7 +909,7 @@ class RichCollectionBase(CollectionBase): 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.") + 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="."): @@ -897,7 +925,8 @@ 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 @@ -916,10 +945,15 @@ 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): @@ -965,7 +999,7 @@ 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: @@ -1008,7 +1042,7 @@ class RichCollectionBase(CollectionBase): """ if changes: - self._committed = False + self.set_committed(False) for change in changes: event_type = change[0] path = change[1] @@ -1049,8 +1083,13 @@ 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): @@ -1091,7 +1130,7 @@ class RichCollectionBase(CollectionBase): @synchronized def flush(self): """Flush bufferblocks to Keep.""" - for e in self.values(): + for e in listvalues(self): e.flush() @@ -1141,7 +1180,8 @@ class Collection(RichCollectionBase): parent=None, apiconfig=None, block_manager=None, - replication_desired=None): + replication_desired=None, + put_threads=None): """Collection constructor. :manifest_locator_or_text: @@ -1178,6 +1218,7 @@ class Collection(RichCollectionBase): 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 @@ -1187,6 +1228,7 @@ 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() @@ -1194,11 +1236,11 @@ 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( @@ -1268,7 +1310,7 @@ class Collection(RichCollectionBase): copies = (self.replication_desired or self._my_api()._rootDesc.get('defaultCollectionReplication', 2)) - self._block_manager = _BlockManager(self._my_keep(), copies=copies) + self._block_manager = _BlockManager(self._my_keep(), copies=copies, put_threads=self.put_threads) return self._block_manager def _remember_api_response(self, response): @@ -1288,6 +1330,7 @@ class Collection(RichCollectionBase): 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: @@ -1303,7 +1346,7 @@ class Collection(RichCollectionBase): # mode. Return an exception, or None if successful. try: self._manifest_text = self._my_keep().get( - self._manifest_locator, num_retries=self.num_retries) + self._manifest_locator, num_retries=self.num_retries).decode() except Exception as e: return e @@ -1313,10 +1356,10 @@ class Collection(RichCollectionBase): error_via_api = None error_via_keep = None should_try_keep = ((self._manifest_text is None) and - util.keep_locator_pattern.match( + arvados.util.keep_locator_pattern.match( self._manifest_locator)) if ((self._manifest_text is None) and - util.signed_locator_pattern.match(self._manifest_locator)): + arvados.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() @@ -1342,7 +1385,7 @@ class Collection(RichCollectionBase): 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 @@ -1453,7 +1496,8 @@ class Collection(RichCollectionBase): ).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 @@ -1511,9 +1555,10 @@ class Collection(RichCollectionBase): 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 @@ -1544,7 +1589,7 @@ class Collection(RichCollectionBase): stream_name = tok.replace('\\040', ' ') blocks = [] segments = [] - streamoffset = 0L + streamoffset = 0 state = BLOCKS self.find_or_create(stream_name, COLLECTION) continue @@ -1552,7 +1597,7 @@ class Collection(RichCollectionBase): if state == BLOCKS: block_locator = re.match(r'[0-9a-f]{32}\+(\d+)(\+\S+)*', 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: @@ -1561,8 +1606,8 @@ class Collection(RichCollectionBase): 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)) + 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) @@ -1578,7 +1623,7 @@ class Collection(RichCollectionBase): stream_name = None state = STREAM_NAME - self.set_committed() + self.set_committed(True) @synchronized def notify(self, event, collection, name, item): @@ -1628,7 +1673,7 @@ 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