X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/112d6ce9132ea6749aef115e3787483958e858fd..c4fa80c6ed2445e1e384455944eb6c4108906cad:/sdk/python/arvados/collection.py?ds=sidebyside diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index 874c38e79e..7bfdf782f8 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -1,28 +1,14 @@ -import gflags -import httplib -import httplib2 +import functools import logging import os -import pprint -import sys -import types -import subprocess -import json -import UserDict import re -import hashlib -import string -import bz2 -import zlib -import fcntl -import time -import threading from collections import deque from stat import * +from .arvfile import ArvadosFileBase from keep import * -from stream import * +from .stream import StreamReader, split import config import errors import util @@ -51,7 +37,7 @@ def normalize_stream(s, stream): fout = f.replace(' ', '\\040') for segment in stream[f]: segmentoffset = blocks[segment[arvados.LOCATOR]] + segment[arvados.OFFSET] - if current_span == None: + if current_span is None: current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]] else: if segmentoffset == current_span[1]: @@ -60,42 +46,20 @@ def normalize_stream(s, stream): 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 != None: + if current_span is not None: stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout)) - if len(stream[f]) == 0: + if not stream[f]: stream_tokens.append("0:0:{0}".format(fout)) return stream_tokens -def normalize(collection): - streams = {} - for s in collection.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])) - - normalized_streams = [] - sortedstreams = list(streams.keys()) - sortedstreams.sort() - for s in sortedstreams: - normalized_streams.append(normalize_stream(s, streams[s])) - return normalized_streams - 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): @@ -104,6 +68,25 @@ class CollectionBase(object): num_retries=self.num_retries) return self._keep_client + def stripped_manifest(self): + """ + 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. + """ + raw = self.manifest_text() + clean = [] + for line in raw.split("\n"): + fields = line.split() + if fields: + clean_fields = fields[:1] + [ + (re.sub(r'\+[^\d][^\+]*', '', x) + if re.match(util.keep_locator_pattern, x) + else x) + for x in fields[1:]] + clean += [' '.join(clean_fields), "\n"] + return ''.join(clean) + class CollectionReader(CollectionBase): def __init__(self, manifest_locator_or_text, api_client=None, @@ -142,38 +125,59 @@ class CollectionReader(CollectionBase): else: raise errors.ArgumentError( "Argument to CollectionReader must be a manifest or a collection UUID") + self._api_response = None 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. + self._api_response = self._api_client.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._streams is not None: - return error_via_api = None error_via_keep = None - should_try_keep = (not self._manifest_text and + should_try_keep = ((self._manifest_text is None) and util.keep_locator_pattern.match( self._manifest_locator)) - if (not self._manifest_text and + if ((self._manifest_text is None) and util.signed_locator_pattern.match(self._manifest_locator)): - try: - self._populate_from_keep() - except e: - error_via_keep = e - if not self._manifest_text: - try: - self._populate_from_api_server() - except Exception as e: - if not should_try_keep: - raise - error_via_api = e - if (not self._manifest_text and + 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 - try: - self._populate_from_keep() - except Exception as e: - error_via_keep = e - if not self._manifest_text: + error_via_keep = self._populate_from_keep() + if self._manifest_text is None: # Nothing worked! raise arvados.errors.NotFoundError( ("Failed to retrieve collection '{}' " + @@ -185,17 +189,75 @@ class CollectionReader(CollectionBase): self._streams = [sline.split() for sline in self._manifest_text.split("\n") if sline] - self._streams = normalize(self) - # now regenerate the manifest text based on the normalized stream - - #print "normalizing", self._manifest_text - self._manifest_text = ''.join([StreamReader(stream, keep=self._my_keep()).manifest_text() for stream in self._streams]) - #print "result", self._manifest_text + def _populate_first(orig_func): + # Decorator for methods that read actual Collection data. + @functools.wraps(orig_func) + def wrapper(self, *args, **kwargs): + if self._streams is None: + self._populate() + return orig_func(self, *args, **kwargs) + return wrapper + + @_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 + @_populate_first + def normalize(self): + # 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[0], r[1])) + + self._streams = [normalize_stream(s, streams[s]) + for s in sorted(streams)] + + # 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]) + + @_populate_first + def open(self, streampath, filename=None): + """open(streampath[, filename]) -> file-like object + + Pass in the path of a file to read from the Collection, either as a + single string or as two separate stream name and file name arguments. + This method returns a file-like object to read that file. + """ + if filename is None: + streampath, filename = split(streampath) + keep_client = self._my_keep() + for stream_s in self._streams: + stream = StreamReader(stream_s, keep_client, + num_retries=self.num_retries) + if stream.name() == streampath: + break + else: + raise ValueError("stream '{}' not found in Collection". + format(streampath)) + try: + return stream.files()[filename] + except KeyError: + raise ValueError("file '{}' not found in Collection stream '{}'". + format(filename, streampath)) + @_populate_first def all_streams(self): - self._populate() return [StreamReader(s, self._my_keep(), num_retries=self.num_retries) for s in self._streams] @@ -204,19 +266,45 @@ class CollectionReader(CollectionBase): for f in s.all_files(): yield f - def manifest_text(self, strip=False): - self._populate() - if strip: - m = ''.join([StreamReader(stream, keep=self._my_keep()).manifest_text(strip=True) for stream in self._streams]) - return m + @_populate_first + 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: return self._manifest_text +class _WriterFile(ArvadosFileBase): + def __init__(self, coll_writer, name): + super(_WriterFile, self).__init__(name, 'wb') + self.dest = coll_writer + + def close(self): + super(_WriterFile, self).close() + self.dest.finish_current_file() + + @ArvadosFileBase._before_close + def write(self, data): + self.dest.write(data) + + @ArvadosFileBase._before_close + def writelines(self, seq): + for data in seq: + self.write(data) + + @ArvadosFileBase._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. @@ -232,9 +320,13 @@ 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 @@ -249,9 +341,11 @@ 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: @@ -308,10 +402,9 @@ class CollectionWriter(CollectionBase): def _work_trees(self): path, stream_name, max_manifest_depth = self._queued_trees[0] - make_dirents = (util.listdir_recursive if (max_manifest_depth == 0) - else os.listdir) - d = make_dirents(path) - if len(d) > 0: + d = util.listdir_recursive( + path, max_depth = (None if max_manifest_depth == 0 else 0)) + if d: self._queue_dirents(stream_name, d) else: self._queued_trees.popleft() @@ -355,11 +448,42 @@ class CollectionWriter(CollectionBase): while self._data_buffer_len >= self.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._my_keep().put( + data_buffer[0:self.KEEP_BLOCK_SIZE], + copies=self.replication)) self._data_buffer = [data_buffer[self.KEEP_BLOCK_SIZE:]] self._data_buffer_len = len(self._data_buffer[0]) @@ -372,13 +496,17 @@ 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): return self._current_file_name def finish_current_file(self): - if self._current_file_name == None: + if self._current_file_name is None: if self._current_file_pos == self._current_stream_length: return raise errors.AssertionError( @@ -430,23 +558,20 @@ 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. - def stripped_manifest(self): - """ - Return the manifest for the current collection with all permission - hints removed from the locators in the manifest. + 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. """ - raw = self.manifest_text() - clean = '' - for line in raw.split("\n"): - fields = line.split() - if len(fields) > 0: - locators = [ re.sub(r'\+A[a-z0-9@_-]+', '', x) - for x in fields[1:-1] ] - clean += fields[0] + ' ' + ' '.join(locators) + ' ' + fields[-1] + "\n" - return clean + return self._my_keep().put(self.manifest_text(), copies=self.replication) + + def portable_data_hash(self): + stripped = self.stripped_manifest() + return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped)) def manifest_text(self): self.finish_current_stream() @@ -460,10 +585,7 @@ class CollectionWriter(CollectionBase): manifest += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2]) manifest += "\n" - if manifest: - return CollectionReader(manifest, self._api_client).manifest_text() - else: - return "" + return manifest def data_locators(self): ret = [] @@ -479,10 +601,9 @@ 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):