X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/9e1d5923421b3439f0cd3297240beebebed38754..c59670ea1fd789bf084b83fb33be3b84312dc07b:/sdk/python/arvados/collection.py diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py index e420a679e2..a86a1f512c 100644 --- a/sdk/python/arvados/collection.py +++ b/sdk/python/arvados/collection.py @@ -27,6 +27,8 @@ import config import errors import util +_logger = logging.getLogger('arvados.collection') + def normalize_stream(s, stream): stream_tokens = [s] sortedfiles = list(stream.keys()) @@ -90,11 +92,16 @@ def normalize(collection): class CollectionReader(object): - def __init__(self, manifest_locator_or_text): - if re.search(r'^[a-f0-9]{32}(\+\d+)?(\+\S+)*$', manifest_locator_or_text): + def __init__(self, manifest_locator_or_text, api_client=None): + self._api_client = api_client + self._keep_client = None + if re.match(r'[a-f0-9]{32}(\+\d+)?(\+\S+)*$', manifest_locator_or_text): + self._manifest_locator = manifest_locator_or_text + self._manifest_text = None + elif re.match(r'[a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}$', manifest_locator_or_text): self._manifest_locator = manifest_locator_or_text self._manifest_text = None - elif re.search(r'^\S+( [a-f0-9]{32,}(\+\S+)*)*( \d+:\d+:\S+)+\n', manifest_locator_or_text): + elif re.match(r'(\S+)( [a-f0-9]{32}(\+\d+)(\+\S+)*)+( \d+:\d+:\S+)+\n', manifest_locator_or_text): self._manifest_text = manifest_locator_or_text self._manifest_locator = None else: @@ -109,17 +116,30 @@ class CollectionReader(object): pass def _populate(self): - if self._streams != None: + if self._streams is not None: return if not self._manifest_text: try: - c = arvados.api('v1').collections().get( + # 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. + if self._api_client is None: + self._api_client = arvados.api('v1') + self._keep_client = KeepClient(api_client=self._api_client) + if self._keep_client is None: + self._keep_client = KeepClient(api_client=self._api_client) + c = self._api_client.collections().get( uuid=self._manifest_locator).execute() self._manifest_text = c['manifest_text'] except Exception as e: - logging.warning("API lookup failed for collection %s (%s: %s)" % - (self._manifest_locator, type(e), str(e))) - self._manifest_text = Keep.get(self._manifest_locator) + _logger.warning("API lookup failed for collection %s (%s: %s)", + self._manifest_locator, type(e), str(e)) + if self._keep_client is None: + self._keep_client = KeepClient(api_client=self._api_client) + self._manifest_text = self._keep_client.get(self._manifest_locator) self._streams = [] for stream_line in self._manifest_text.split("\n"): if stream_line != '': @@ -157,7 +177,9 @@ class CollectionReader(object): class CollectionWriter(object): KEEP_BLOCK_SIZE = 2**26 - def __init__(self): + def __init__(self, api_client=None): + self._api_client = api_client + self._keep_client = None self._data_buffer = [] self._data_buffer_len = 0 self._current_stream_files = [] @@ -178,6 +200,10 @@ class CollectionWriter(object): 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 do_queued_work(self): # The work queue consists of three pieces: # * _queued_file: The file object we're currently writing to the @@ -283,7 +309,9 @@ class CollectionWriter(object): def flush_data(self): data_buffer = ''.join(self._data_buffer) if data_buffer != '': - self._current_stream_locators += [Keep.put(data_buffer[0:self.KEEP_BLOCK_SIZE])] + self._prep_keep_client() + self._current_stream_locators.append( + self._keep_client.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]) @@ -312,8 +340,8 @@ class CollectionWriter(object): 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_length - self._current_file_pos, + self._current_file_name]] self._current_file_pos = self._current_stream_length def start_new_stream(self, newstreamname='.'): @@ -342,8 +370,8 @@ class CollectionWriter(object): 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]] + self._current_stream_locators, + self._current_stream_files]] self._current_stream_files = [] self._current_stream_length = 0 self._current_stream_locators = [] @@ -352,9 +380,9 @@ class CollectionWriter(object): self._current_file_name = None def finish(self): - # Send the stripped manifest to Keep, to ensure that we use the - # same UUID regardless of what hints are used on the collection. - return Keep.put(self.stripped_manifest()) + # Store the manifest in Keep and return its locator. + self._prep_keep_client() + return self._keep_client.put(self.manifest_text()) def stripped_manifest(self): """ @@ -402,9 +430,9 @@ class ResumableCollectionWriter(CollectionWriter): '_data_buffer', '_dependencies', '_finished_streams', '_queued_dirents', '_queued_trees'] - def __init__(self): + def __init__(self, api_client=None): self._dependencies = {} - super(ResumableCollectionWriter, self).__init__() + super(ResumableCollectionWriter, self).__init__(api_client) @classmethod def from_state(cls, state, *init_args, **init_kwargs):