X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b2610e066d569b323fe55ffee615e61ca4e461d1..c4fa80c6ed2445e1e384455944eb6c4108906cad:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index e6ab42437d..7bfdf782f8 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -1,26 +1,14 @@ -import gflags +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 @@ -69,9 +57,9 @@ def normalize_stream(s, stream): 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): @@ -137,6 +125,7 @@ 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): @@ -151,10 +140,10 @@ class CollectionReader(CollectionBase): 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( + self._api_response = self._api_client.collections().get( uuid=self._manifest_locator).execute( num_retries=self.num_retries) - self._manifest_text = c['manifest_text'] + self._manifest_text = self._api_response['manifest_text'] return None except Exception as e: return e @@ -171,8 +160,6 @@ class CollectionReader(CollectionBase): 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 @@ -203,17 +190,32 @@ class CollectionReader(CollectionBase): for sline in self._manifest_text.split("\n") if sline] - def normalize(self): - self._populate() + 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(): - filestream = s.name() + "/" + f.name() - r = filestream.rindex("/") - streamname = filestream[:r] - filename = filestream[r+1:] + streamname, filename = split(s.name() + "/" + f.name()) if streamname not in streams: streams[streamname] = {} if filename not in streams[streamname]: @@ -229,8 +231,33 @@ class CollectionReader(CollectionBase): [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] @@ -239,6 +266,7 @@ class CollectionReader(CollectionBase): for f in s.all_files(): yield f + @_populate_first def manifest_text(self, strip=False, normalize=False): if normalize: cr = CollectionReader(self.manifest_text()) @@ -247,14 +275,36 @@ class CollectionReader(CollectionBase): elif strip: return self.stripped_manifest() else: - self._populate() 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. @@ -270,9 +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 @@ -287,9 +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: @@ -392,11 +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]) @@ -409,6 +496,10 @@ 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 +558,16 @@ 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 +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):