X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b0e2fe9d0a18d5e809bc8c0d3382e0e023cb949c..04f5f75659e963f02441a566afcc6d22683d0485:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index 24572edf56..ea18123f65 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -2,13 +2,15 @@ import functools import logging import os import re +import errno from collections import deque from stat import * -from .arvfile import ArvadosFileBase, split +from .arvfile import ArvadosFileBase, split, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, BlockManager from keep import * -from .stream import StreamReader, normalize_stream +from .stream import StreamReader, normalize_stream, locator_block_size +from .ranges import Range, LocatorAndRange import config import errors import util @@ -181,7 +183,7 @@ class CollectionReader(CollectionBase): if filename not in streams[streamname]: streams[streamname][filename] = [] for r in f.segments: - streams[streamname][filename].extend(s.locators_and_ranges(r[0], r[1])) + streams[streamname][filename].extend(s.locators_and_ranges(r.locator, r.range_size)) self._streams = [normalize_stream(s, streams[s]) for s in sorted(streams)] @@ -636,3 +638,413 @@ class ResumableCollectionWriter(CollectionWriter): raise errors.AssertionError( "resumable writer can't accept unsourced data") return super(ResumableCollectionWriter, self).write(data) + + +class Collection(CollectionBase): + def __init__(self, manifest_locator_or_text=None, parent=None, api_client=None, + keep_client=None, num_retries=0, block_manager=None): + + self.parent = parent + self._items = None + self._api_client = api_client + self._keep_client = keep_client + self._block_manager = block_manager + + self.num_retries = num_retries + self._manifest_locator = None + self._manifest_text = None + self._api_response = None + + if manifest_locator_or_text: + if re.match(util.keep_locator_pattern, manifest_locator_or_text): + self._manifest_locator = manifest_locator_or_text + elif re.match(util.collection_uuid_pattern, manifest_locator_or_text): + self._manifest_locator = manifest_locator_or_text + elif re.match(util.manifest_pattern, manifest_locator_or_text): + self._manifest_text = manifest_locator_or_text + else: + raise errors.ArgumentError( + "Argument to CollectionReader must be a manifest or a collection UUID") + + def _my_api(self): + if self._api_client is None: + if self.parent is not None: + return self.parent._my_api() + self._api_client = arvados.api('v1') + self._keep_client = None # Make a new one with the new api. + return self._api_client + + def _my_keep(self): + if self._keep_client is None: + if self.parent is not None: + return self.parent._my_keep() + self._keep_client = KeepClient(api_client=self._my_api(), + num_retries=self.num_retries) + return self._keep_client + + def _my_block_manager(self): + if self._block_manager is None: + if self.parent is not None: + return self.parent._my_block_manager() + self._block_manager = BlockManager(self._my_keep()) + return self._block_manager + + def _populate_from_api_server(self): + # As in KeepClient itself, we must wait until the last + # possible moment to instantiate an API client, in order to + # avoid tripping up clients that don't have access to an API + # server. If we do build one, make sure our Keep client uses + # it. If instantiation fails, we'll fall back to the except + # clause, just like any other Collection lookup + # failure. Return an exception, or None if successful. + try: + self._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 + + def _populate(self): + self._items = {} + 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 arvados.errors.NotFoundError( + ("Failed to retrieve collection '{}' " + + "from either API server ({}) or Keep ({})." + ).format( + self._manifest_locator, + error_via_api, + error_via_keep)) + # populate + import_manifest(self._manifest_text, self) + + def _populate_first(orig_func): + # Decorator for methods that read actual Collection data. + @functools.wraps(orig_func) + def wrapper(self, *args, **kwargs): + if self._items is None: + self._populate() + return orig_func(self, *args, **kwargs) + return wrapper + + def __enter__(self): + return self + + def __exit__(self, exc_type, exc_value, traceback): + self.save(no_locator=True) + if self._block_manager is not None: + self._block_manager.stop_threads() + + @_populate_first + def find(self, path, create=False, create_collection=False): + p = path.split("/") + if p[0] == '.': + del p[0] + + if len(p) > 0: + item = self._items.get(p[0]) + if len(p) == 1: + # item must be a file + if item is None and create: + # create new file + if create_collection: + item = Collection(parent=self, num_retries=self.num_retries) + else: + item = ArvadosFile(self) + self._items[p[0]] = item + return item + else: + if item is None and create: + # create new collection + item = Collection(parent=self, num_retries=self.num_retries) + self._items[p[0]] = item + del p[0] + return item.find("/".join(p), create=create) + else: + return self + + @_populate_first + def api_response(self): + """api_response() -> dict or None + + Returns information about this Collection fetched from the API server. + If the Collection exists in Keep but not the API server, currently + returns None. Future versions may provide a synthetic response. + """ + return self._api_response + + def open(self, path, mode): + mode = mode.replace("b", "") + if len(mode) == 0 or mode[0] not in ("r", "w", "a"): + raise ArgumentError("Bad mode '%s'" % mode) + create = (mode != "r") + + f = self.find(path, create=create) + if f is None: + raise IOError((errno.ENOENT, "File not found")) + if not isinstance(f, ArvadosFile): + raise IOError((errno.EISDIR, "Path must refer to a file.")) + + if mode[0] == "w": + f.truncate(0) + + if mode == "r": + return ArvadosFileReader(f, path, mode) + else: + return ArvadosFileWriter(f, path, mode) + + @_populate_first + def modified(self): + for k,v in self._items.items(): + if v.modified(): + return True + return False + + @_populate_first + def set_unmodified(self): + for k,v in self._items.items(): + v.set_unmodified() + + @_populate_first + def __iter__(self): + return self._items.iterkeys() + + @_populate_first + def iterkeys(self): + return self._items.iterkeys() + + @_populate_first + def __getitem__(self, k): + return self._items[k] + + @_populate_first + def __contains__(self, k): + return k in self._items + + @_populate_first + def __len__(self): + return len(self._items) + + @_populate_first + def __delitem__(self, p): + del self._items[p] + + @_populate_first + def keys(self): + return self._items.keys() + + @_populate_first + def values(self): + return self._items.values() + + @_populate_first + def items(self): + return self._items.items() + + @_populate_first + def exists(self, path): + return self.find(path) != None + + @_populate_first + def remove(self, path): + p = path.split("/") + if p[0] == '.': + del p[0] + + if len(p) > 0: + item = self._items.get(p[0]) + if item is None: + raise IOError((errno.ENOENT, "File not found")) + if len(p) == 1: + del self._items[p[0]] + else: + del p[0] + item.remove("/".join(p)) + else: + raise IOError((errno.ENOENT, "File not found")) + + @_populate_first + def manifest_text(self, strip=False, normalize=False): + if self.modified() or self._manifest_text is None or normalize: + return export_manifest(self, stream_name=".", portable_locators=strip) + else: + if strip: + return self.stripped_manifest() + else: + return self._manifest_text + + def portable_data_hash(self): + stripped = self.manifest_text(strip=True) + return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped)) + + @_populate_first + def save(self, no_locator=False): + if self.modified(): + self._my_block_manager().commit_all() + self._my_keep().put(self.manifest_text(strip=True)) + if self._manifest_locator is not None and re.match(util.collection_uuid_pattern, self._manifest_locator): + self._api_response = self._my_api().collections().update( + uuid=self._manifest_locator, + body={'manifest_text': self.manifest_text(strip=False)} + ).execute( + num_retries=self.num_retries) + elif not no_locator: + raise AssertionError("Collection manifest_locator must be a collection uuid. Use save_as() for new collections.") + self.set_unmodified() + + @_populate_first + def save_as(self, name, owner_uuid=None, ensure_unique_name=False): + self._my_block_manager().commit_all() + self._my_keep().put(self.manifest_text(strip=True)) + body = {"manifest_text": self.manifest_text(strip=False), + "name": name} + 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=self.num_retries) + self._manifest_locator = self._api_response["uuid"] + self.set_unmodified() + + @_populate_first + def rename(self, old, new): + old_path, old_fn = os.path.split(old) + old_col = self.find(path) + if old_col is None: + raise IOError((errno.ENOENT, "File not found")) + if not isinstance(old_p, Collection): + raise IOError((errno.ENOTDIR, "Parent in path is a file, not a directory")) + if old_fn in old_col: + new_path, new_fn = os.path.split(new) + new_col = self.find(new_path, create=True, create_collection=True) + if not isinstance(new_col, Collection): + raise IOError((errno.ENOTDIR, "Destination is a file, not a directory")) + ent = old_col[old_fn] + del old_col[old_fn] + ent.parent = new_col + new_col[new_fn] = ent + else: + raise IOError((errno.ENOENT, "File not found")) + +def import_manifest(manifest_text, into_collection=None, api_client=None, keep=None, num_retries=None): + if into_collection is not None: + if len(into_collection) > 0: + raise ArgumentError("Can only import manifest into an empty collection") + c = into_collection + else: + c = Collection(api_client=api_client, keep_client=keep, num_retries=num_retries) + + STREAM_NAME = 0 + BLOCKS = 1 + SEGMENTS = 2 + + stream_name = None + state = STREAM_NAME + + for n in re.finditer(r'(\S+)(\s+|$)', manifest_text): + tok = n.group(1) + sep = n.group(2) + + if state == STREAM_NAME: + # starting a new stream + stream_name = tok.replace('\\040', ' ') + blocks = [] + segments = [] + streamoffset = 0L + state = BLOCKS + continue + + if state == BLOCKS: + s = re.match(r'[0-9a-f]{32}\+(\d+)(\+\S+)*', tok) + if s: + blocksize = long(s.group(1)) + blocks.append(Range(tok, streamoffset, blocksize)) + streamoffset += blocksize + else: + state = SEGMENTS + + if state == SEGMENTS: + s = re.search(r'^(\d+):(\d+):(\S+)', tok) + if s: + pos = long(s.group(1)) + size = long(s.group(2)) + name = s.group(3).replace('\\040', ' ') + f = c.find("%s/%s" % (stream_name, name), create=True) + f.add_segment(blocks, pos, size) + else: + # error! + raise errors.SyntaxError("Invalid manifest format") + + if sep == "\n": + stream_name = None + state = STREAM_NAME + + c.set_unmodified() + return c + +def export_manifest(item, stream_name=".", portable_locators=False): + buf = "" + if isinstance(item, Collection): + stream = {} + sorted_keys = sorted(item.keys()) + for k in [s for s in sorted_keys if isinstance(item[s], ArvadosFile)]: + v = item[k] + st = [] + for s in v.segments: + loc = s.locator + if loc.startswith("bufferblock"): + loc = v.parent._my_block_manager()._bufferblocks[loc].locator() + if portable_locators: + loc = KeepLocator(loc).stripped() + st.append(LocatorAndRange(loc, locator_block_size(loc), + s.segment_offset, s.range_size)) + stream[k] = st + if stream: + buf += ' '.join(normalize_stream(stream_name, stream)) + buf += "\n" + for k in [s for s in sorted_keys if isinstance(item[s], Collection)]: + buf += export_manifest(item[k], stream_name=os.path.join(stream_name, k), portable_locators=portable_locators) + elif isinstance(item, ArvadosFile): + st = [] + for s in item.segments: + loc = s.locator + if loc.startswith("bufferblock"): + loc = item._bufferblocks[loc].calculate_locator() + if portable_locators: + loc = KeepLocator(loc).stripped() + st.append(LocatorAndRange(loc, locator_block_size(loc), + s.segment_offset, s.range_size)) + stream[stream_name] = st + buf += ' '.join(normalize_stream(stream_name, stream)) + buf += "\n" + return buf