X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5141c3ee23e89696773e227a93236ef2a51543c2..c4fa80c6ed2445e1e384455944eb6c4108906cad:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index fa782a1ac2..7bfdf782f8 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -1,3 +1,4 @@ +import functools import logging import os import re @@ -124,6 +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): @@ -138,10 +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 @@ -158,8 +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 @@ -190,9 +190,27 @@ 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(): @@ -213,6 +231,7 @@ 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 @@ -220,7 +239,6 @@ class CollectionReader(CollectionBase): single string or as two separate stream name and file name arguments. This method returns a file-like object to read that file. """ - self._populate() if filename is None: streampath, filename = split(streampath) keep_client = self._my_keep() @@ -238,8 +256,8 @@ class CollectionReader(CollectionBase): 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] @@ -248,6 +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()) @@ -256,7 +275,6 @@ class CollectionReader(CollectionBase): elif strip: return self.stripped_manifest() else: - self._populate() return self._manifest_text @@ -286,7 +304,7 @@ class _WriterFile(ArvadosFileBase): 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. @@ -302,9 +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 @@ -459,7 +481,9 @@ class CollectionWriter(CollectionBase): 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]) @@ -472,6 +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): @@ -530,8 +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() @@ -565,10 +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):