X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e82cddfdbd763db27df889a6e316623df7b9c2a8..63b03a39adfd78961c5bbb6a3a2d02ccd8c92e4d:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index e6ab42437d..b0cdd92251 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -1,77 +1,34 @@ -import gflags +import functools import logging import os -import pprint -import sys -import types -import subprocess -import json -import UserDict import re +import errno import hashlib -import string -import bz2 -import zlib -import fcntl import time import threading from collections import deque from stat import * -from keep import * -from stream import * +from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, _BlockManager, synchronized, must_be_writable, NoopLock +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 +from arvados.retry import retry_method _logger = logging.getLogger('arvados.collection') -def normalize_stream(s, stream): - stream_tokens = [s] - sortedfiles = list(stream.keys()) - sortedfiles.sort() - - blocks = {} - streamoffset = 0L - for f in sortedfiles: - for b in stream[f]: - if b[arvados.LOCATOR] not in blocks: - stream_tokens.append(b[arvados.LOCATOR]) - blocks[b[arvados.LOCATOR]] = streamoffset - streamoffset += b[arvados.BLOCKSIZE] - - if len(stream_tokens) == 1: - stream_tokens.append(config.EMPTY_BLOCK_LOCATOR) - - for f in sortedfiles: - current_span = None - fout = f.replace(' ', '\\040') - for segment in stream[f]: - segmentoffset = blocks[segment[arvados.LOCATOR]] + segment[arvados.OFFSET] - if current_span is None: - current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]] - else: - if segmentoffset == current_span[1]: - current_span[1] += segment[arvados.SEGMENTSIZE] - else: - stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout)) - current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]] - - if current_span is not None: - stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout)) - - if not stream[f]: - stream_tokens.append("0:0:{0}".format(fout)) - - return stream_tokens - - class CollectionBase(object): def __enter__(self): - pass + return self - def __exit__(self): + def __exit__(self, exc_type, exc_value, traceback): pass def _my_keep(self): @@ -81,7 +38,8 @@ class CollectionBase(object): return self._keep_client def stripped_manifest(self): - """ + """Get the manifest with locator hints stripped. + Return the manifest for the current collection with all non-portable hints (i.e., permission signatures and other hints other than size hints) removed from the locators. @@ -100,161 +58,31 @@ class CollectionBase(object): return ''.join(clean) -class CollectionReader(CollectionBase): - def __init__(self, manifest_locator_or_text, api_client=None, - keep_client=None, num_retries=0): - """Instantiate a CollectionReader. - - This class parses Collection manifests to provide a simple interface - to read its underlying files. - - Arguments: - * manifest_locator_or_text: One of a Collection UUID, portable data - hash, or full manifest text. - * api_client: The API client to use to look up Collections. If not - provided, CollectionReader will build one from available Arvados - configuration. - * keep_client: The KeepClient to use to download Collection data. - If not provided, CollectionReader will build one from available - Arvados configuration. - * num_retries: The default number of times to retry failed - service requests. Default 0. You may change this value - after instantiation, but note those changes may not - propagate to related objects like the Keep client. - """ - self._api_client = api_client - self._keep_client = keep_client - self.num_retries = num_retries - if re.match(util.keep_locator_pattern, manifest_locator_or_text): - self._manifest_locator = manifest_locator_or_text - self._manifest_text = None - elif re.match(util.collection_uuid_pattern, manifest_locator_or_text): - self._manifest_locator = manifest_locator_or_text - self._manifest_text = None - elif re.match(util.manifest_pattern, manifest_locator_or_text): - self._manifest_text = manifest_locator_or_text - self._manifest_locator = None - else: - raise errors.ArgumentError( - "Argument to CollectionReader must be a manifest or a collection UUID") - self._streams = None - - 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: - if self._api_client is None: - self._api_client = arvados.api('v1') - self._keep_client = None # Make a new one with the new api. - c = self._api_client.collections().get( - uuid=self._manifest_locator).execute( - num_retries=self.num_retries) - self._manifest_text = c['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): - if self._streams is not 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)) - self._streams = [sline.split() - for sline in self._manifest_text.split("\n") - if sline] - - def normalize(self): - self._populate() - - # Rearrange streams - streams = {} - for s in self.all_streams(): - for f in s.all_files(): - filestream = s.name() + "/" + f.name() - r = filestream.rindex("/") - streamname = filestream[:r] - filename = filestream[r+1:] - if streamname not in streams: - streams[streamname] = {} - 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])) - - self._streams = [normalize_stream(s, streams[s]) - for s in sorted(streams)] +class _WriterFile(_FileLikeObjectBase): + def __init__(self, coll_writer, name): + super(_WriterFile, self).__init__(name, 'wb') + self.dest = coll_writer - # Regenerate the manifest text based on the normalized streams - self._manifest_text = ''.join( - [StreamReader(stream, keep=self._my_keep()).manifest_text() - for stream in self._streams]) + def close(self): + super(_WriterFile, self).close() + self.dest.finish_current_file() - def all_streams(self): - self._populate() - return [StreamReader(s, self._my_keep(), num_retries=self.num_retries) - for s in self._streams] + @_FileLikeObjectBase._before_close + def write(self, data): + self.dest.write(data) - def all_files(self): - for s in self.all_streams(): - for f in s.all_files(): - yield f + @_FileLikeObjectBase._before_close + def writelines(self, seq): + for data in seq: + self.write(data) - def manifest_text(self, strip=False, normalize=False): - if normalize: - cr = CollectionReader(self.manifest_text()) - cr.normalize() - return cr.manifest_text(strip=strip, normalize=False) - elif strip: - return self.stripped_manifest() - else: - self._populate() - return self._manifest_text + @_FileLikeObjectBase._before_close + def flush(self): + self.dest.flush_data() class CollectionWriter(CollectionBase): - KEEP_BLOCK_SIZE = 2**26 - - def __init__(self, api_client=None, num_retries=0): + def __init__(self, api_client=None, num_retries=0, replication=None): """Instantiate a CollectionWriter. CollectionWriter lets you build a new Arvados Collection from scratch. @@ -270,9 +98,13 @@ class CollectionWriter(CollectionBase): service requests. Default 0. You may change this value after instantiation, but note those changes may not propagate to related objects like the Keep client. + * replication: The number of copies of each block to store. + If this argument is None or not supplied, replication is + the server-provided default if available, otherwise 2. """ self._api_client = api_client self.num_retries = num_retries + self.replication = (2 if replication is None else replication) self._keep_client = None self._data_buffer = [] self._data_buffer_len = 0 @@ -287,9 +119,11 @@ class CollectionWriter(CollectionBase): self._queued_file = None self._queued_dirents = deque() self._queued_trees = deque() + self._last_open = None - def __exit__(self): - self.finish() + def __exit__(self, exc_type, exc_value, traceback): + if exc_type is None: + self.finish() def do_queued_work(self): # The work queue consists of three pieces: @@ -317,7 +151,7 @@ class CollectionWriter(CollectionBase): def _work_file(self): while True: - buf = self._queued_file.read(self.KEEP_BLOCK_SIZE) + buf = self._queued_file.read(config.KEEP_BLOCK_SIZE) if not buf: break self.write(buf) @@ -389,15 +223,46 @@ class CollectionWriter(CollectionBase): self._data_buffer.append(newdata) self._data_buffer_len += len(newdata) self._current_stream_length += len(newdata) - while self._data_buffer_len >= self.KEEP_BLOCK_SIZE: + while self._data_buffer_len >= config.KEEP_BLOCK_SIZE: self.flush_data() + def open(self, streampath, filename=None): + """open(streampath[, filename]) -> file-like object + + Pass in the path of a file to write to the Collection, either as a + single string or as two separate stream name and file name arguments. + This method returns a file-like object you can write to add it to the + Collection. + + You may only have one file object from the Collection open at a time, + so be sure to close the object when you're done. Using the object in + a with statement makes that easy:: + + with cwriter.open('./doc/page1.txt') as outfile: + outfile.write(page1_data) + with cwriter.open('./doc/page2.txt') as outfile: + outfile.write(page2_data) + """ + if filename is None: + 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( + filename, self._last_open.name)) + if streampath != self.current_stream_name(): + self.start_new_stream(streampath) + self.set_current_file_name(filename) + self._last_open = _WriterFile(self, filename) + return self._last_open + def flush_data(self): data_buffer = ''.join(self._data_buffer) if data_buffer: self._current_stream_locators.append( - self._my_keep().put(data_buffer[0:self.KEEP_BLOCK_SIZE])) - self._data_buffer = [data_buffer[self.KEEP_BLOCK_SIZE:]] + self._my_keep().put( + data_buffer[0:config.KEEP_BLOCK_SIZE], + copies=self.replication)) + self._data_buffer = [data_buffer[config.KEEP_BLOCK_SIZE:]] self._data_buffer_len = len(self._data_buffer[0]) def start_new_file(self, newfilename=None): @@ -409,6 +274,10 @@ class CollectionWriter(CollectionBase): raise errors.AssertionError( "Manifest filenames cannot contain whitespace: %s" % newfilename) + elif re.search(r'\x00', newfilename): + raise errors.AssertionError( + "Manifest filenames cannot contain NUL characters: %s" % + newfilename) self._current_file_name = newfilename def current_file_name(self): @@ -467,8 +336,16 @@ class CollectionWriter(CollectionBase): self._current_file_name = None def finish(self): - # Store the manifest in Keep and return its locator. - return self._my_keep().put(self.manifest_text()) + """Store the manifest in Keep and return its locator. + + This is useful for storing manifest fragments (task outputs) + temporarily in Keep during a Crunch job. + + In other cases you should make a collection instead, by + sending manifest_text() to the API server's "create + collection" endpoint. + """ + return self._my_keep().put(self.manifest_text(), copies=self.replication) def portable_data_hash(self): stripped = self.stripped_manifest() @@ -502,10 +379,9 @@ class ResumableCollectionWriter(CollectionWriter): '_data_buffer', '_dependencies', '_finished_streams', '_queued_dirents', '_queued_trees'] - def __init__(self, api_client=None, num_retries=0): + def __init__(self, api_client=None, **kwargs): self._dependencies = {} - super(ResumableCollectionWriter, self).__init__( - api_client, num_retries=num_retries) + super(ResumableCollectionWriter, self).__init__(api_client, **kwargs) @classmethod def from_state(cls, state, *init_args, **init_kwargs): @@ -593,3 +469,1049 @@ class ResumableCollectionWriter(CollectionWriter): raise errors.AssertionError( "resumable writer can't accept unsourced data") return super(ResumableCollectionWriter, self).write(data) + +ADD = "add" +DEL = "del" +MOD = "mod" +FILE = "file" +COLLECTION = "collection" + +class SynchronizedCollectionBase(CollectionBase): + """Base class for Collections and Subcollections. + + Implements the majority of functionality relating to accessing items in the + Collection. + + """ + + def __init__(self, parent=None): + self.parent = parent + self._modified = True + self._items = {} + + def _my_api(self): + raise NotImplementedError() + + def _my_keep(self): + raise NotImplementedError() + + def _my_block_manager(self): + raise NotImplementedError() + + def writable(self): + raise NotImplementedError() + + def root_collection(self): + raise NotImplementedError() + + def notify(self, event, collection, name, item): + raise NotImplementedError() + + def stream_name(self): + raise NotImplementedError() + + @must_be_writable + @synchronized + def find_or_create(self, path, create_type): + """Recursively search the specified file path. + + May return either a `Collection` or `ArvadosFile`. If not found, will + create a new item at the specified path based on `create_type`. Will + create intermediate subcollections needed to contain the final item in + the path. + + :create_type: + One of `arvados.collection.FILE` or + `arvados.collection.COLLECTION`. If the path is not found, and value + of create_type is FILE then create and return a new ArvadosFile for + the last path component. If COLLECTION, then create and return a new + Collection for the last path component. + + """ + + pathcomponents = path.split("/", 1) + if pathcomponents[0]: + item = self._items.get(pathcomponents[0]) + if len(pathcomponents) == 1: + if item is None: + # create new file + if create_type == COLLECTION: + item = Subcollection(self) + else: + item = ArvadosFile(self) + self._items[pathcomponents[0]] = item + self._modified = True + self.notify(ADD, self, pathcomponents[0], item) + return item + else: + if item is None: + # create new collection + item = Subcollection(self) + self._items[pathcomponents[0]] = item + self._modified = True + self.notify(ADD, self, pathcomponents[0], item) + if isinstance(item, SynchronizedCollectionBase): + return item.find_or_create(pathcomponents[1], create_type) + else: + raise IOError((errno.ENOTDIR, "Interior path components must be subcollection")) + else: + return self + + @synchronized + def find(self, path): + """Recursively search the specified file path. + + May return either a Collection or ArvadosFile. Return None if not + found. + + """ + if not path: + raise errors.ArgumentError("Parameter 'path' must not be empty.") + + pathcomponents = path.split("/", 1) + item = self._items.get(pathcomponents[0]) + if len(pathcomponents) == 1: + return item + else: + if isinstance(item, SynchronizedCollectionBase): + if pathcomponents[1]: + return item.find(pathcomponents[1]) + else: + return item + else: + raise IOError((errno.ENOTDIR, "Interior path components must be subcollection")) + + def mkdirs(path): + """Recursive subcollection create. + + Like `os.mkdirs()`. Will create intermediate subcollections needed to + contain the leaf subcollection path. + + """ + return self.find_or_create(path, COLLECTION) + + def open(self, path, mode="r"): + """Open a file-like object for access. + + :path: + path to a file in the collection + :mode: + one of "r", "r+", "w", "w+", "a", "a+" + :"r": + opens for reading + :"r+": + opens for reading and writing. Reads/writes share a file pointer. + :"w", "w+": + truncates to 0 and opens for reading and writing. Reads/writes share a file pointer. + :"a", "a+": + opens for reading and writing. All writes are appended to + 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 create: + arvfile = self.find_or_create(path, FILE) + else: + arvfile = self.find(path) + + if arvfile is None: + raise IOError((errno.ENOENT, "File not found")) + if not isinstance(arvfile, ArvadosFile): + raise IOError((errno.EISDIR, "Path must refer to a file.")) + + if mode[0] == "w": + arvfile.truncate(0) + + name = os.path.basename(path) + + if mode == "r": + return ArvadosFileReader(arvfile, name, mode, num_retries=self.num_retries) + else: + return ArvadosFileWriter(arvfile, name, mode, num_retries=self.num_retries) + + @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 + + @synchronized + def set_unmodified(self): + """Recursively clear modified flag.""" + self._modified = False + for k,v in self._items.items(): + v.set_unmodified() + + @synchronized + def __iter__(self): + """Iterate over names of files and collections contained in this collection.""" + return iter(self._items.keys()) + + @synchronized + def __getitem__(self, k): + """Get a file or collection that is directly contained by this collection. + + If you want to search a path, use `find()` instead. + + """ + return self._items[k] + + @synchronized + def __contains__(self, k): + """Test if there is a file or collection a directly contained by this collection.""" + return k in self._items + + @synchronized + def __len__(self): + """Get the number of items directly contained in this collection.""" + return len(self._items) + + @must_be_writable + @synchronized + def __delitem__(self, p): + """Delete an item by name which is directly contained by this collection.""" + del self._items[p] + self._modified = True + self.notify(DEL, self, p, None) + + @synchronized + def keys(self): + """Get a list of names of files and collections directly contained in this collection.""" + return self._items.keys() + + @synchronized + def values(self): + """Get a list of files and collection objects directly contained in this collection.""" + return self._items.values() + + @synchronized + def items(self): + """Get a list of (name, object) tuples directly contained in this collection.""" + return self._items.items() + + def exists(self, path): + """Test if there is a file or collection at `path`.""" + return self.find(path) != None + + @must_be_writable + @synchronized + def remove(self, path, recursive=False): + """Remove the file or subcollection (directory) at `path`. + + :recursive: + Specify whether to remove non-empty subcollections (True), or raise an error (False). + """ + + if not path: + raise errors.ArgumentError("Parameter 'path' must not be empty.") + + pathcomponents = path.split("/", 1) + item = self._items.get(pathcomponents[0]) + if item is None: + raise IOError((errno.ENOENT, "File not found")) + if len(pathcomponents) == 1: + if isinstance(self._items[pathcomponents[0]], SynchronizedCollectionBase) and len(self._items[pathcomponents[0]]) > 0 and not recursive: + raise IOError((errno.ENOTEMPTY, "Subcollection not empty")) + deleteditem = self._items[pathcomponents[0]] + del self._items[pathcomponents[0]] + self._modified = True + 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) + + 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. + + :source_obj: + An ArvadosFile, or Subcollection object + + :target_name: + Destination item name. If the target name already exists and is a + file, this will raise an error unless you specify `overwrite=True`. + + :overwrite: + Whether to overwrite target file if it already exists. + + """ + + if target_name in self and not overwrite: + raise IOError((errno.EEXIST, "File already exists")) + + 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 + + if modified_from: + self.notify(MOD, self, target_name, (modified_from, dup)) + else: + self.notify(ADD, self, target_name, dup) + + + @must_be_writable + @synchronized + def copy(self, source, target_path, source_collection=None, overwrite=False): + """Copy a file or subcollection to a new path in this collection. + + :source: + A string with a path to source file or subcollection, or an actual ArvadosFile or Subcollection object. + + :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`. + + :source_collection: + Collection to copy `source_path` from (default `self`) + + :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 + + # 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 sourcecomponents else None) + + if not target_name: + raise errors.ArgumentError("Target path is empty and source is an object. Cannot determine destination filename to use.") + + target_dir = self.find_or_create("/".join(targetcomponents[0:-1]), COLLECTION) + + if target_name in target_dir and isinstance(self[target_name], SynchronizedCollectionBase) and sourcecomponents: + target_dir = target_dir[target_name] + target_name = sourcecomponents[-1] + + target_dir.add(source_obj, target_name, overwrite) + + @synchronized + def manifest_text(self, stream_name=".", strip=False, normalize=False): + """Get the manifest text for this collection, sub collections and files. + + :stream_name: + Name of the stream (directory) + + :strip: + If True, remove signing tokens from block locators if present. + If False (default), block locators are left unchanged. + + :normalize: + If True, always export the manifest text in normalized form + even if the Collection is not modified. If False (default) and the collection + is not modified, return the original manifest text even if it is not + in normalized form. + + """ + + if self.modified() or self._manifest_text is None or normalize: + item = self + stream = {} + buf = [] + sorted_keys = sorted(item.keys()) + for filename in [s for s in sorted_keys if isinstance(item[s], ArvadosFile)]: + # Create a stream per file `k` + arvfile = item[filename] + filestream = [] + for segment in arvfile.segments(): + loc = segment.locator + if arvfile.parent._my_block_manager().is_bufferblock(loc): + loc = arvfile.parent._my_block_manager().get_bufferblock(loc).locator() + if strip: + loc = KeepLocator(loc).stripped() + filestream.append(LocatorAndRange(loc, KeepLocator(loc).size, + segment.segment_offset, segment.range_size)) + stream[filename] = filestream + if stream: + buf.append(" ".join(normalize_stream(stream_name, stream)) + "\n") + for dirname in [s for s in sorted_keys if isinstance(item[s], SynchronizedCollectionBase)]: + buf.append(item[dirname].manifest_text(stream_name=os.path.join(stream_name, dirname), strip=strip)) + return "".join(buf) + else: + if strip: + return self.stripped_manifest() + else: + return self._manifest_text + + @synchronized + def diff(self, end_collection, prefix=".", holding_collection=None): + """Generate list of add/modify/delete actions. + + When given to `apply`, will change `self` to match `end_collection` + + """ + changes = [] + if holding_collection is None: + 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))) + 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))) + else: + changes.append((ADD, os.path.join(prefix, k), end_collection[k].clone(holding_collection))) + return changes + + @must_be_writable + @synchronized + def apply(self, changes): + """Apply changes from `diff`. + + If a change conflicts with a local change, it will be saved to an + alternate path indicating the conflict. + + """ + 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", + time.gmtime())) + if event_type == ADD: + if local is None: + # No local file at path, safe to copy over new file + self.copy(initial, path) + elif local is not None and local != initial: + # There is already local file and it is different: + # save change to conflict file. + self.copy(initial, conflictpath) + elif event_type == MOD: + final = change[3] + if local == initial: + # Local matches the "initial" item so it has not + # changed locally and is safe to update. + if isinstance(local, ArvadosFile) and isinstance(final, ArvadosFile): + # Replace contents of local file with new contents + local.replace_contents(final) + else: + # Overwrite path with new item; this can happen if + # path was a file and is now a collection or vice versa + self.copy(final, path, overwrite=True) + else: + # Local is missing (presumably deleted) or local doesn't + # match the "start" value, so save change to conflict file + self.copy(final, conflictpath) + elif event_type == DEL: + if local == initial: + # Local item matches "initial" value, so it is safe to remove. + self.remove(path, recursive=True) + # else, the file is modified or already removed, in either + # case we don't want to try to remove it. + + def portable_data_hash(self): + """Get the portable data hash for this collection's manifest.""" + stripped = self.manifest_text(strip=True) + return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped)) + + @synchronized + def __eq__(self, other): + if other is self: + return True + if not isinstance(other, SynchronizedCollectionBase): + return False + if len(self._items) != len(other): + return False + for k in self._items: + if k not in other: + return False + if self._items[k] != other[k]: + return False + return True + + def __ne__(self, other): + return not self.__eq__(other) + + +class Collection(SynchronizedCollectionBase): + """Represents the root of an Arvados Collection. + + This class is threadsafe. The root collection object, all subcollections + and files are protected by a single lock (i.e. each access locks the entire + collection). + + Brief summary of + useful methods: + + :To read an existing file: + `c.open("myfile", "r")` + + :To write a new file: + `c.open("myfile", "w")` + + :To determine if a file exists: + `c.find("myfile") is not None` + + :To copy a file: + `c.copy("source", "dest")` + + :To delete a file: + `c.remove("myfile")` + + :To save to an existing collection record: + `c.save()` + + :To save a new collection record: + `c.save_new()` + + :To merge remote changes into this object: + `c.update()` + + Must be associated with an API server Collection record (during + initialization, or using `save_new`) to use `save` or `update` + + """ + + def __init__(self, manifest_locator_or_text=None, + api_client=None, + keep_client=None, + num_retries=None, + parent=None, + apiconfig=None, + block_manager=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). + :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. + + """ + super(Collection, self).__init__(parent) + self._api_client = api_client + self._keep_client = keep_client + self._block_manager = block_manager + + if apiconfig: + self._config = apiconfig + else: + self._config = config.settings() + + self.num_retries = num_retries if num_retries is not None else 0 + self._manifest_locator = None + self._manifest_text = None + self._api_response = None + + 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): + 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") + + try: + self._populate() + except (IOError, errors.SyntaxError) as e: + raise errors.ArgumentError("Error processing manifest text: %s", e) + + def root_collection(self): + return self + + def stream_name(self): + return "." + + def writable(self): + return True + + @synchronized + @retry_method + def update(self, other=None, num_retries=None): + """Merge the latest collection on the API server with the current collection.""" + + if other is None: + 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) + other = CollectionReader(response["manifest_text"]) + baseline = CollectionReader(self._manifest_text) + self.apply(baseline.diff(other)) + + @synchronized + def _my_api(self): + if self._api_client is None: + self._api_client = ThreadSafeApiCache(self._config) + self._keep_client = self._api_client.keep + return self._api_client + + @synchronized + def _my_keep(self): + if self._keep_client is None: + if self._api_client is None: + self._my_api() + else: + self._keep_client = KeepClient(api_client=self._api_client) + return self._keep_client + + @synchronized + def _my_block_manager(self): + if self._block_manager is None: + 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): + 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 + 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) + + 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 self.writable() and self._has_collection_uuid(): + self.save() + if self._block_manager is not None: + self._block_manager.stop_threads() + + @synchronized + def manifest_locator(self): + """Get the manifest locator. May be None.""" + return self._manifest_locator + + @synchronized + def clone(self, new_parent=None, readonly=False, new_config=None): + if new_config is None: + new_config = self._config + if readonly: + newcollection = CollectionReader(parent=new_parent, apiconfig=new_config) + else: + newcollection = Collection(parent=new_parent, apiconfig=new_config) + + newcollection._clonefrom(self) + return newcollection + + @synchronized + def api_response(self): + """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 find_or_create(self, path, create_type): + """See `SynchronizedCollectionBase.find_or_create`""" + if path == ".": + return self + else: + return super(Collection, self).find_or_create(path[2:] if path.startswith("./") else path, create_type) + + def find(self, path): + """See `SynchronizedCollectionBase.find`""" + if path == ".": + return self + else: + return super(Collection, self).find(path[2:] if path.startswith("./") else path) + + def remove(self, path, recursive=False): + """See `SynchronizedCollectionBase.remove`""" + if path == ".": + raise errors.ArgumentError("Cannot remove '.'") + else: + return super(Collection, self).remove(path[2:] if path.startswith("./") else path, recursive) + + @must_be_writable + @synchronized + @retry_method + def save(self, merge=True, num_retries=None): + """Save collection to an existing collection record. + + Commit pending buffer blocks to Keep, merge with remote record (if + update=True), write the manifest to Keep, and update the collection + record. + + 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()`. + + :merge: + Update and merge remote changes before saving. Otherwise, any + remote changes will be ignored and overwritten. + + :num_retries: + Retry count on API calls (if None, use the collection default) + + """ + if self.modified(): + if not self._has_collection_uuid(): + raise AssertionError("Collection manifest_locator must be a collection uuid. Use save_new() for new collections.") + self._my_block_manager().commit_all() + if merge: + self.update() + self._my_keep().put(self.manifest_text(strip=True), num_retries=num_retries) + + text = self.manifest_text(strip=False) + self._api_response = self._my_api().collections().update( + uuid=self._manifest_locator, + body={'manifest_text': text} + ).execute( + num_retries=num_retries) + self._manifest_text = self._api_response["manifest_text"] + self.set_unmodified() + + + @must_be_writable + @synchronized + @retry_method + def save_new(self, name=None, create_collection_record=True, owner_uuid=None, ensure_unique_name=False, num_retries=None): + """Save collection to a new collection record. + + Commit pending buffer blocks to Keep, write the manifest to Keep, and + create a new collection record (if create_collection_record True). + After creating a new collection record, this Collection object will be + associated with the new record used by `save()`. + + :name: + The collection name. + + :create_collection_record: + If True, create a collection record. If False, only save the manifest to keep. + + :owner_uuid: + the user, or project uuid that will own this collection. + If None, defaults to the current user. + + :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 + False, a name conflict will result in an error. + + :num_retries: + Retry count on API calls (if None, use the collection default) + + """ + self._my_block_manager().commit_all() + self._my_keep().put(self.manifest_text(strip=True), num_retries=num_retries) + 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())) + + body = {"manifest_text": text, + "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=num_retries) + text = self._api_response["manifest_text"] + + self._manifest_locator = self._api_response["uuid"] + + self._manifest_text = text + self.set_unmodified() + + @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) + + @synchronized + def _import_manifest(self, manifest_text): + """Import a manifest into a `Collection`. + + :manifest_text: + The manifest text to import from. + + """ + if len(self) > 0: + raise ArgumentError("Can only import manifest into an empty collection") + + STREAM_NAME = 0 + BLOCKS = 1 + SEGMENTS = 2 + + stream_name = None + state = STREAM_NAME + + for token_and_separator in re.finditer(r'(\S+)(\s+|$)', manifest_text): + tok = token_and_separator.group(1) + sep = token_and_separator.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: + block_locator = re.match(r'[0-9a-f]{32}\+(\d+)(\+\S+)*', tok) + if block_locator: + blocksize = long(block_locator.group(1)) + blocks.append(Range(tok, streamoffset, blocksize)) + streamoffset += blocksize + else: + state = SEGMENTS + + 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)) + name = file_segment.group(3).replace('\\040', ' ') + filepath = os.path.join(stream_name, name) + afile = self.find_or_create(filepath, FILE) + if isinstance(afile, ArvadosFile): + afile.add_segment(blocks, pos, size) + else: + raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath) + else: + # error! + raise errors.SyntaxError("Invalid manifest format") + + if sep == "\n": + stream_name = None + state = STREAM_NAME + + self.set_unmodified() + + +class Subcollection(SynchronizedCollectionBase): + """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. + + """ + + def __init__(self, parent): + super(Subcollection, self).__init__(parent) + self.lock = self.root_collection().lock + self._manifest_text = None + + def root_collection(self): + return self.parent.root_collection() + + def writable(self): + return self.root_collection().writable() + + def _my_api(self): + return self.root_collection()._my_api() + + def _my_keep(self): + return self.root_collection()._my_keep() + + 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 '.' + + @synchronized + def clone(self, new_parent): + c = Subcollection(new_parent) + c._clonefrom(self) + return c + + +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. + + """ + def __init__(self, manifest_locator_or_text, *args, **kwargs): + self._in_init = True + super(CollectionReader, self).__init__(manifest_locator_or_text, *args, **kwargs) + self._in_init = False + + # Forego any locking since it should never change once initialized. + self.lock = NoopLock() + + # Backwards compatability with old CollectionReader + # all_streams() and all_files() + self._streams = None + + def writable(self): + return self._in_init + + def _populate_streams(orig_func): + @functools.wraps(orig_func) + def populate_streams_wrapper(self, *args, **kwargs): + # Defer populating self._streams until needed since it creates a copy of the manifest. + if self._streams is None: + if self._manifest_text: + self._streams = [sline.split() + for sline in self._manifest_text.split("\n") + if sline] + else: + self._streams = [] + return orig_func(self, *args, **kwargs) + return populate_streams_wrapper + + @_populate_streams + def normalize(self): + """Normalize the streams returned by `all_streams`. + + This method is kept for backwards compatability and only affects the + behavior of `all_streams()` and `all_files()` + + """ + + # Rearrange streams + streams = {} + for s in self.all_streams(): + for f in s.all_files(): + streamname, filename = split(s.name() + "/" + f.name()) + if streamname not in streams: + streams[streamname] = {} + if filename not in streams[streamname]: + streams[streamname][filename] = [] + for r in f.segments: + 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)] + @_populate_streams + def all_streams(self): + return [StreamReader(s, self._my_keep(), num_retries=self.num_retries) + for s in self._streams] + + @_populate_streams + def all_files(self): + for s in self.all_streams(): + for f in s.all_files(): + yield f