X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d9e48a19b82fe1d957686e0803c759553666237e..0b0b4c7b23e96a6efb3cfd88b0ba7224158e9544:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index 48fdaf03ec..44d0325353 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -7,24 +7,26 @@ from future.utils import listitems, listvalues, viewkeys from builtins import str from past.builtins import basestring from builtins import object +import ciso8601 +import datetime +import errno import functools +import hashlib +import io import logging import os import re -import errno -import hashlib -import datetime -import ciso8601 -import time +import sys import threading +import time from collections import deque from stat import * -from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, _BlockManager, synchronized, must_be_writable, NoopLock +from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, WrappableFile, _BlockManager, synchronized, must_be_writable, NoopLock from .keep import KeepLocator, KeepClient from .stream import StreamReader -from ._normalize_stream import normalize_stream +from ._normalize_stream import normalize_stream, escape from ._ranges import Range, LocatorAndRange from .safeapi import ThreadSafeApiCache import arvados.config as config @@ -35,6 +37,21 @@ from arvados.retry import retry_method _logger = logging.getLogger('arvados.collection') + +if sys.version_info >= (3, 0): + TextIOWrapper = io.TextIOWrapper +else: + class TextIOWrapper(io.TextIOWrapper): + """To maintain backward compatibility, cast str to unicode in + write('foo'). + + """ + def write(self, data): + if isinstance(data, basestring): + data = unicode(data) + return super(TextIOWrapper, self).write(data) + + class CollectionBase(object): """Abstract base class for Collection classes.""" @@ -266,7 +283,7 @@ class CollectionWriter(CollectionBase): 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( + u"can't open '{}' when '{}' is still open".format( filename, self._last_open.name)) if streampath != self.current_stream_name(): self.start_new_stream(streampath) @@ -444,22 +461,22 @@ class ResumableCollectionWriter(CollectionWriter): writer._queued_file.seek(pos) except IOError as error: raise errors.StaleWriterStateError( - "failed to reopen active file {}: {}".format(path, error)) + u"failed to reopen active file {}: {}".format(path, error)) return writer def check_dependencies(self): for path, orig_stat in listitems(self._dependencies): if not S_ISREG(orig_stat[ST_MODE]): - raise errors.StaleWriterStateError("{} not file".format(path)) + raise errors.StaleWriterStateError(u"{} not file".format(path)) try: now_stat = tuple(os.stat(path)) except OSError as error: raise errors.StaleWriterStateError( - "failed to stat {}: {}".format(path, error)) + u"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)) + raise errors.StaleWriterStateError(u"{} changed".format(path)) def dump_state(self, copy_func=lambda x: x): state = {attr: copy_func(getattr(self, attr)) @@ -475,7 +492,7 @@ class ResumableCollectionWriter(CollectionWriter): try: src_path = os.path.realpath(source) except Exception: - raise errors.AssertionError("{} not a file path".format(source)) + raise errors.AssertionError(u"{} not a file path".format(source)) try: path_stat = os.stat(src_path) except OSError as stat_error: @@ -488,10 +505,10 @@ class ResumableCollectionWriter(CollectionWriter): self._dependencies[source] = tuple(fd_stat) elif path_stat is None: raise errors.AssertionError( - "could not stat {}: {}".format(source, stat_error)) + u"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)) + u"{} changed between open and stat calls".format(source)) else: self._dependencies[src_path] = tuple(fd_stat) @@ -545,6 +562,7 @@ class RichCollectionBase(CollectionBase): def stream_name(self): raise NotImplementedError() + @synchronized def has_remote_blocks(self): """Recursively check for a +R segment locator signature.""" @@ -654,7 +672,7 @@ class RichCollectionBase(CollectionBase): return self.find_or_create(path, COLLECTION) - def open(self, path, mode="r"): + def open(self, path, mode="r", encoding=None): """Open a file-like object for access. :path: @@ -676,6 +694,7 @@ class RichCollectionBase(CollectionBase): opens for reading and writing. All writes are appended to the end of the file. Writing does not affect the file pointer for reading. + """ if not re.search(r'^[rwa][bt]?\+?$', mode): @@ -698,7 +717,12 @@ class RichCollectionBase(CollectionBase): if mode[0] == 'w': arvfile.truncate(0) - return fclass(arvfile, mode=mode, num_retries=self.num_retries) + binmode = mode[0] + 'b' + re.sub('[bt]', '', mode[1:]) + f = fclass(arvfile, mode=binmode, num_retries=self.num_retries) + if 'b' not in mode: + bufferclass = io.BufferedRandom if f.writable() else io.BufferedReader + f = TextIOWrapper(bufferclass(WrappableFile(f)), encoding=encoding) + return f def modified(self): """Determine if the collection has been modified since last commited.""" @@ -1035,7 +1059,9 @@ 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, only_committed=only_committed)) + 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: @@ -1235,6 +1261,7 @@ class Collection(RichCollectionBase): apiconfig=None, block_manager=None, replication_desired=None, + storage_classes_desired=None, put_threads=None): """Collection constructor. @@ -1267,12 +1294,22 @@ class Collection(RichCollectionBase): configuration applies. If not None, this value will also be used for determining the number of block copies being written. + :storage_classes_desired: + A list of storage class names where to upload the data. If None, + the keepstores are expected to store the data into their default + storage class. + """ + + if storage_classes_desired and type(storage_classes_desired) is not list: + raise errors.ArgumentError("storage_classes_desired must be list type.") + 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._storage_classes_desired = storage_classes_desired self.put_threads = put_threads if apiconfig: @@ -1310,6 +1347,9 @@ class Collection(RichCollectionBase): except (IOError, errors.SyntaxError) as e: raise errors.ArgumentError("Error processing manifest text: %s", e) + def storage_classes_desired(self): + return self._storage_classes_desired or [] + def root_collection(self): return self @@ -1321,7 +1361,10 @@ class Collection(RichCollectionBase): def get_trash_at(self): if self._api_response and self._api_response["trash_at"]: - return ciso8601.parse_datetime(self._api_response["trash_at"]) + try: + return ciso8601.parse_datetime(self._api_response["trash_at"]) + except ValueError: + return None else: return None @@ -1381,7 +1424,7 @@ class Collection(RichCollectionBase): copies = (self.replication_desired or self._my_api()._rootDesc.get('defaultCollectionReplication', 2)) - self._block_manager = _BlockManager(self._my_keep(), copies=copies, put_threads=self.put_threads) + self._block_manager = _BlockManager(self._my_keep(), copies=copies, put_threads=self.put_threads, num_retries=self.num_retries, storage_classes_func=self.storage_classes_desired) return self._block_manager def _remember_api_response(self, response): @@ -1402,9 +1445,11 @@ class Collection(RichCollectionBase): 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 + # replication_desired and storage_classes_desired from the API server if self.replication_desired is None: self.replication_desired = self._api_response.get('replication_desired', None) + if self._storage_classes_desired is None: + self._storage_classes_desired = self._api_response.get('storage_classes_desired', None) def _populate(self): if self._manifest_text is None: @@ -1537,6 +1582,8 @@ class Collection(RichCollectionBase): if storage_classes and type(storage_classes) is not list: raise errors.ArgumentError("storage_classes must be list type.") + if storage_classes: + self._storage_classes_desired = storage_classes if trash_at and type(trash_at) is not datetime.datetime: raise errors.ArgumentError("trash_at must be datetime type.") @@ -1544,8 +1591,8 @@ class Collection(RichCollectionBase): body={} if properties: body["properties"] = properties - if storage_classes: - body["storage_classes_desired"] = storage_classes + if self.storage_classes_desired(): + body["storage_classes_desired"] = self.storage_classes_desired() if trash_at: t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ") body["trash_at"] = t @@ -1648,6 +1695,9 @@ class Collection(RichCollectionBase): self._copy_remote_blocks(remote_blocks={}) self._has_remote_blocks = False + if storage_classes: + self._storage_classes_desired = storage_classes + self._my_block_manager().commit_all() text = self.manifest_text(strip=False) @@ -1663,8 +1713,8 @@ class Collection(RichCollectionBase): body["owner_uuid"] = owner_uuid if properties: body["properties"] = properties - if storage_classes: - body["storage_classes_desired"] = storage_classes + if self.storage_classes_desired(): + body["storage_classes_desired"] = self.storage_classes_desired() if trash_at: t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ") body["trash_at"] = t @@ -1810,6 +1860,16 @@ class Subcollection(RichCollectionBase): self.name = newname self.lock = self.parent.root_collection().lock + @synchronized + def _get_manifest_text(self, stream_name, strip, normalize, only_committed=False): + """Encode empty directories by using an \056-named (".") empty file""" + if len(self._items) == 0: + return "%s %s 0:0:\\056\n" % ( + escape(stream_name), config.EMPTY_BLOCK_LOCATOR) + return super(Subcollection, self)._get_manifest_text(stream_name, + strip, normalize, + only_committed) + class CollectionReader(Collection): """A read-only collection object.