X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/327e1768a130476a411baf4cd4fb602f7a73c5ed..7924077e3db2898de26c86599d9f311e02d6db46:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index 40b5889c31..59dc49fbbc 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -1,22 +1,6 @@ -import gflags -import httplib -import httplib2 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 * @@ -51,7 +35,7 @@ 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]: @@ -60,45 +44,80 @@ 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 CollectionReader(object): - def __init__(self, manifest_locator_or_text, api_client=None): + +class CollectionBase(object): + def __enter__(self): + return self + + def __exit__(self, exc_type, exc_value, traceback): + pass + + def _my_keep(self): + if self._keep_client is None: + self._keep_client = KeepClient(api_client=self._api_client, + 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, + 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 = None - if re.match(r'[a-f0-9]{32}(\+\d+)?(\+\S+)*$', manifest_locator_or_text): + 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(r'(\S+)( [a-f0-9]{32}(\+\d+)(\+\S+)*)+( \d+:\d+:\S+)+\n', manifest_locator_or_text): + 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: @@ -106,67 +125,140 @@ class CollectionReader(object): "Argument to CollectionReader must be a manifest or a collection UUID") self._streams = None - def __enter__(self): - pass - - def __exit__(self): - pass + 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 - if not self._manifest_text: - if self._api_client is None: - self._api_client = arvados.api('v1') - if self._keep_client is None: - self._keep_client = KeepClient(api_client=self._api_client) - try: - c = self._api_client.collections().get( - uuid=self._manifest_locator).execute() - self._manifest_text = c['manifest_text'] - except Exception as e: - _logger.warning("API lookup failed for collection %s (%s: %s)", - self._manifest_locator, type(e), str(e)) - self._manifest_text = self._keep_client.get(self._manifest_locator) - self._streams = [] - for stream_line in self._manifest_text.split("\n"): - if stream_line != '': - stream_tokens = stream_line.split() - self._streams += [stream_tokens] - 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).manifest_text() for stream in self._streams]) - #print "result", self._manifest_text + 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)] + + # 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 all_streams(self): self._populate() - resp = [] - for s in self._streams: - resp.append(StreamReader(s)) - return resp + return [StreamReader(s, self._my_keep(), num_retries=self.num_retries) + for s in self._streams] def all_files(self): for s in self.all_streams(): for f in s.all_files(): yield f - def manifest_text(self, strip=False): - self._populate() - if strip: - m = ''.join([StreamReader(stream).manifest_text(strip=True) for stream in self._streams]) - return m + 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 -class CollectionWriter(object): + +class CollectionWriter(CollectionBase): KEEP_BLOCK_SIZE = 2**26 - def __init__(self, api_client=None): + def __init__(self, api_client=None, num_retries=0): + """Instantiate a CollectionWriter. + + CollectionWriter lets you build a new Arvados Collection from scratch. + Write files to it. The CollectionWriter will upload data to Keep as + appropriate, and provide you with the Collection manifest text when + you're finished. + + Arguments: + * api_client: The API client to use to look up Collections. 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.num_retries = num_retries self._keep_client = None self._data_buffer = [] self._data_buffer_len = 0 @@ -182,15 +274,9 @@ class CollectionWriter(object): self._queued_dirents = deque() self._queued_trees = deque() - def __enter__(self): - pass - - def __exit__(self): - self.finish() - - def _prep_keep_client(self): - if self._keep_client is None: - self._keep_client = KeepClient(api_client=self._api_client) + 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: @@ -247,10 +333,9 @@ class CollectionWriter(object): 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() @@ -288,7 +373,7 @@ class CollectionWriter(object): for s in newdata: self.write(s) return - self._data_buffer += [newdata] + 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: @@ -296,10 +381,9 @@ class CollectionWriter(object): def flush_data(self): data_buffer = ''.join(self._data_buffer) - if data_buffer != '': - self._prep_keep_client() + if data_buffer: self._current_stream_locators.append( - self._keep_client.put(data_buffer[0:self.KEEP_BLOCK_SIZE])) + self._my_keep().put(data_buffer[0:self.KEEP_BLOCK_SIZE])) self._data_buffer = [data_buffer[self.KEEP_BLOCK_SIZE:]] self._data_buffer_len = len(self._data_buffer[0]) @@ -318,7 +402,7 @@ class CollectionWriter(object): 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( @@ -327,10 +411,12 @@ class CollectionWriter(object): (self._current_stream_length - self._current_file_pos, self._current_file_pos, self._current_stream_name)) - self._current_stream_files += [[self._current_file_pos, - self._current_stream_length - self._current_file_pos, - self._current_file_name]] + self._current_stream_files.append([ + self._current_file_pos, + self._current_stream_length - self._current_file_pos, + self._current_file_name]) self._current_file_pos = self._current_stream_length + self._current_file_name = None def start_new_stream(self, newstreamname='.'): self.finish_current_stream() @@ -348,18 +434,18 @@ class CollectionWriter(object): def finish_current_stream(self): self.finish_current_file() self.flush_data() - if len(self._current_stream_files) == 0: + if not self._current_stream_files: pass - elif self._current_stream_name == None: + elif self._current_stream_name is None: raise errors.AssertionError( "Cannot finish an unnamed stream (%d bytes in %d files)" % (self._current_stream_length, len(self._current_stream_files))) else: - if len(self._current_stream_locators) == 0: - self._current_stream_locators += [config.EMPTY_BLOCK_LOCATOR] - self._finished_streams += [[self._current_stream_name, - self._current_stream_locators, - self._current_stream_files]] + if not self._current_stream_locators: + self._current_stream_locators.append(config.EMPTY_BLOCK_LOCATOR) + self._finished_streams.append([self._current_stream_name, + self._current_stream_locators, + self._current_stream_files]) self._current_stream_files = [] self._current_stream_length = 0 self._current_stream_locators = [] @@ -369,23 +455,11 @@ class CollectionWriter(object): def finish(self): # Store the manifest in Keep and return its locator. - self._prep_keep_client() - return self._keep_client.put(self.manifest_text()) + return self._my_keep().put(self.manifest_text()) - def stripped_manifest(self): - """ - Return the manifest for the current collection with all permission - hints removed from the locators in the manifest. - """ - 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 + 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() @@ -399,10 +473,7 @@ class CollectionWriter(object): manifest += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2]) manifest += "\n" - if len(manifest) > 0: - return CollectionReader(manifest).manifest_text() - else: - return "" + return manifest def data_locators(self): ret = [] @@ -418,9 +489,10 @@ class ResumableCollectionWriter(CollectionWriter): '_data_buffer', '_dependencies', '_finished_streams', '_queued_dirents', '_queued_trees'] - def __init__(self, api_client=None): + def __init__(self, api_client=None, num_retries=0): self._dependencies = {} - super(ResumableCollectionWriter, self).__init__(api_client) + super(ResumableCollectionWriter, self).__init__( + api_client, num_retries=num_retries) @classmethod def from_state(cls, state, *init_args, **init_kwargs):