Module arvados.collection
Classes
class Collection (manifest_locator_or_text=None, api_client=None, keep_client=None, num_retries=None, parent=None, apiconfig=None, block_manager=None, replication_desired=None, storage_classes_desired=None, put_threads=None, get_threads=None)-
Represents the root of an Arvados Collection.
This class is threadsafe. The root collection object, all subcollections and files are protected by a single lock (i.e. each access locks the entire collection).
Brief summary of useful methods:
:To read an existing file:
c.open("myfile", "r"):To write a new file:
c.open("myfile", "w"):To determine if a file exists:
c.find("myfile") is not None:To copy a file:
c.copy("source", "dest"):To delete a file:
c.remove("myfile"):To save to an existing collection record:
c.save():To save a new collection record:
c.save_new():To merge remote changes into this object:
c.update()Must be associated with an API server Collection record (during initialization, or using
save_new) to usesaveorupdateCollection constructor.
:manifest_locator_or_text: An Arvados collection UUID, portable data hash, raw manifest text, or (if creating an empty collection) None.
:parent: the parent Collection, may be None.
:apiconfig: A dict containing keys for ARVADOS_API_HOST and ARVADOS_API_TOKEN. Prefer this over supplying your own api_client and keep_client (except in testing). Will use default config settings if not specified.
:api_client: The API client object to use for requests. If not specified, create one using
apiconfig.:keep_client: the Keep client to use for requests. If not specified, create one using
apiconfig.:num_retries: the number of retries for API and Keep requests.
:block_manager: the block manager to use. If not specified, create one.
:replication_desired: How many copies should Arvados maintain. If None, API server default configuration applies. If not None, this value will also be used for determining the number of block copies being written.
:storage_classes_desired: A list of storage class names where to upload the data. If None, the keep client is expected to store the data into the cluster's default storage class(es).
Expand source code
class Collection(RichCollectionBase): """Represents the root of an Arvados Collection. This class is threadsafe. The root collection object, all subcollections and files are protected by a single lock (i.e. each access locks the entire collection). Brief summary of useful methods: :To read an existing file: `c.open("myfile", "r")` :To write a new file: `c.open("myfile", "w")` :To determine if a file exists: `c.find("myfile") is not None` :To copy a file: `c.copy("source", "dest")` :To delete a file: `c.remove("myfile")` :To save to an existing collection record: `c.save()` :To save a new collection record: `c.save_new()` :To merge remote changes into this object: `c.update()` Must be associated with an API server Collection record (during initialization, or using `save_new`) to use `save` or `update` """ def __init__(self, manifest_locator_or_text=None, api_client=None, keep_client=None, num_retries=None, parent=None, apiconfig=None, block_manager=None, replication_desired=None, storage_classes_desired=None, put_threads=None, get_threads=None): """Collection constructor. :manifest_locator_or_text: An Arvados collection UUID, portable data hash, raw manifest text, or (if creating an empty collection) None. :parent: the parent Collection, may be None. :apiconfig: A dict containing keys for ARVADOS_API_HOST and ARVADOS_API_TOKEN. Prefer this over supplying your own api_client and keep_client (except in testing). Will use default config settings if not specified. :api_client: The API client object to use for requests. If not specified, create one using `apiconfig`. :keep_client: the Keep client to use for requests. If not specified, create one using `apiconfig`. :num_retries: the number of retries for API and Keep requests. :block_manager: the block manager to use. If not specified, create one. :replication_desired: How many copies should Arvados maintain. If None, API server default configuration applies. If not None, this value will also be used for determining the number of block copies being written. :storage_classes_desired: A list of storage class names where to upload the data. If None, the keep client is expected to store the data into the cluster's default storage class(es). """ if storage_classes_desired and type(storage_classes_desired) is not list: raise errors.ArgumentError("storage_classes_desired must be list type.") super(Collection, self).__init__(parent) self._api_client = api_client self._keep_client = keep_client # Use the keep client from ThreadSafeApiCache if self._keep_client is None and isinstance(self._api_client, ThreadSafeApiCache): self._keep_client = self._api_client.keep self._block_manager = block_manager self.replication_desired = replication_desired self._storage_classes_desired = storage_classes_desired self.put_threads = put_threads self.get_threads = get_threads if apiconfig: self._config = apiconfig else: self._config = config.settings() self.num_retries = num_retries if num_retries is not None else 0 self._manifest_locator = None self._manifest_text = None self._portable_data_hash = None self._api_response = None self._past_versions = set() self.lock = threading.RLock() self.events = None if manifest_locator_or_text: if re.match(arvados.util.keep_locator_pattern, manifest_locator_or_text): self._manifest_locator = manifest_locator_or_text elif re.match(arvados.util.collection_uuid_pattern, manifest_locator_or_text): self._manifest_locator = manifest_locator_or_text if not self._has_local_collection_uuid(): self._has_remote_blocks = True elif re.match(arvados.util.manifest_pattern, manifest_locator_or_text): self._manifest_text = manifest_locator_or_text if '+R' in self._manifest_text: self._has_remote_blocks = True else: raise errors.ArgumentError( "Argument to CollectionReader is not a manifest or a collection UUID") try: self._populate() except errors.SyntaxError as e: raise errors.ArgumentError("Error processing manifest text: %s", str(e)) from None def storage_classes_desired(self): return self._storage_classes_desired or [] def root_collection(self): return self def get_properties(self): if self._api_response and self._api_response["properties"]: return self._api_response["properties"] else: return {} def get_trash_at(self): if self._api_response and self._api_response["trash_at"]: try: return ciso8601.parse_datetime(self._api_response["trash_at"]) except ValueError: return None else: return None def stream_name(self): return "." def writable(self): return True @synchronized def known_past_version(self, modified_at_and_portable_data_hash): return modified_at_and_portable_data_hash in self._past_versions @synchronized @retry_method def update(self, other=None, num_retries=None): """Merge the latest collection on the API server with the current collection.""" if other is None: if self._manifest_locator is None: raise errors.ArgumentError("`other` is None but collection does not have a manifest_locator uuid") response = self._my_api().collections().get(uuid=self._manifest_locator).execute(num_retries=num_retries) if (self.known_past_version((response.get("modified_at"), response.get("portable_data_hash"))) and response.get("portable_data_hash") != self.portable_data_hash()): # The record on the server is different from our current one, but we've seen it before, # so ignore it because it's already been merged. # However, if it's the same as our current record, proceed with the update, because we want to update # our tokens. return else: self._remember_api_response(response) other = CollectionReader(response["manifest_text"]) baseline = CollectionReader(self._manifest_text) self.apply(baseline.diff(other)) self._manifest_text = self.manifest_text() @synchronized def _my_api(self): if self._api_client is None: self._api_client = ThreadSafeApiCache(self._config, version='v1') if self._keep_client is None: self._keep_client = self._api_client.keep return self._api_client @synchronized def _my_keep(self): if self._keep_client is None: if self._api_client is None: self._my_api() else: self._keep_client = KeepClient(api_client=self._api_client) return self._keep_client @synchronized def _my_block_manager(self): if self._block_manager is None: copies = (self.replication_desired or self._my_api()._rootDesc.get('defaultCollectionReplication', 2)) self._block_manager = _BlockManager(self._my_keep(), copies=copies, put_threads=self.put_threads, num_retries=self.num_retries, storage_classes_func=self.storage_classes_desired, get_threads=self.get_threads,) return self._block_manager def _remember_api_response(self, response): self._api_response = response self._past_versions.add((response.get("modified_at"), response.get("portable_data_hash"))) 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. self._remember_api_response(self._my_api().collections().get( uuid=self._manifest_locator).execute( num_retries=self.num_retries)) self._manifest_text = self._api_response['manifest_text'] self._portable_data_hash = self._api_response['portable_data_hash'] # If not overriden via kwargs, we should try to load the # replication_desired and storage_classes_desired from the API server if self.replication_desired is None: self.replication_desired = self._api_response.get('replication_desired', None) if self._storage_classes_desired is None: self._storage_classes_desired = self._api_response.get('storage_classes_desired', None) def _populate(self): if self._manifest_text is None: if self._manifest_locator is None: return else: self._populate_from_api_server() self._baseline_manifest = self._manifest_text self._import_manifest(self._manifest_text) def _has_collection_uuid(self): return self._manifest_locator is not None and re.match(arvados.util.collection_uuid_pattern, self._manifest_locator) def _has_local_collection_uuid(self): return self._has_collection_uuid and \ self._my_api()._rootDesc['uuidPrefix'] == self._manifest_locator.split('-')[0] def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): """Support scoped auto-commit in a with: block.""" if exc_type is None: if self.writable() and self._has_collection_uuid(): self.save() self.stop_threads() def stop_threads(self): if self._block_manager is not None: self._block_manager.stop_threads() @synchronized def manifest_locator(self): """Get the manifest locator, if any. The manifest locator will be set when the collection is loaded from an API server record or the portable data hash of a manifest. The manifest locator will be None if the collection is newly created or was created directly from manifest text. The method `save_new()` will assign a manifest locator. """ return self._manifest_locator @synchronized def clone(self, new_parent=None, new_name=None, readonly=False, new_config=None): if new_config is None: new_config = self._config if readonly: newcollection = CollectionReader(parent=new_parent, apiconfig=new_config) else: newcollection = Collection(parent=new_parent, apiconfig=new_config) newcollection._clonefrom(self) return newcollection @synchronized def api_response(self): """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 def find_or_create(self, path, create_type): """See `RichCollectionBase.find_or_create`""" if path == ".": return self else: return super(Collection, self).find_or_create(path[2:] if path.startswith("./") else path, create_type) def find(self, path): """See `RichCollectionBase.find`""" if path == ".": return self else: return super(Collection, self).find(path[2:] if path.startswith("./") else path) def remove(self, path, recursive=False): """See `RichCollectionBase.remove`""" if path == ".": raise errors.ArgumentError("Cannot remove '.'") else: return super(Collection, self).remove(path[2:] if path.startswith("./") else path, recursive) @must_be_writable @synchronized @retry_method def save(self, properties=None, storage_classes=None, trash_at=None, merge=True, num_retries=None, preserve_version=False): """Save collection to an existing collection record. Commit pending buffer blocks to Keep, merge with remote record (if merge=True, the default), and update the collection record. Returns the current manifest text. Will raise AssertionError if not associated with a collection record on the API server. If you want to save a manifest to Keep only, see `save_new()`. :properties: Additional properties of collection. This value will replace any existing properties of collection. :storage_classes: Specify desirable storage classes to be used when writing data to Keep. :trash_at: A collection is *expiring* when it has a *trash_at* time in the future. An expiring collection can be accessed as normal, but is scheduled to be trashed automatically at the *trash_at* time. :merge: Update and merge remote changes before saving. Otherwise, any remote changes will be ignored and overwritten. :num_retries: Retry count on API calls (if None, use the collection default) :preserve_version: If True, indicate that the collection content being saved right now should be preserved in a version snapshot if the collection record is updated in the future. Requires that the API server has Collections.CollectionVersioning enabled, if not, setting this will raise an exception. """ if properties and type(properties) is not dict: raise errors.ArgumentError("properties must be dictionary type.") if storage_classes and type(storage_classes) is not list: raise errors.ArgumentError("storage_classes must be list type.") if storage_classes: self._storage_classes_desired = storage_classes if trash_at and type(trash_at) is not datetime.datetime: raise errors.ArgumentError("trash_at must be datetime type.") if preserve_version and not self._my_api().config()['Collections'].get('CollectionVersioning', False): raise errors.ArgumentError("preserve_version is not supported when CollectionVersioning is not enabled.") body={} if properties: body["properties"] = properties if self.storage_classes_desired(): body["storage_classes_desired"] = self.storage_classes_desired() if trash_at: t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ") body["trash_at"] = t if preserve_version: body["preserve_version"] = preserve_version if not self.committed(): if self._has_remote_blocks: # Copy any remote blocks to the local cluster. self._copy_remote_blocks(remote_blocks={}) self._has_remote_blocks = False if not self._has_collection_uuid(): raise AssertionError("Collection manifest_locator is not a collection uuid. Use save_new() for new collections.") elif not self._has_local_collection_uuid(): raise AssertionError("Collection manifest_locator is from a remote cluster. Use save_new() to save it on the local cluster.") self._my_block_manager().commit_all() if merge: self.update() text = self.manifest_text(strip=False) body['manifest_text'] = text self._remember_api_response(self._my_api().collections().update( uuid=self._manifest_locator, body=body ).execute(num_retries=num_retries)) self._manifest_text = self._api_response["manifest_text"] self._portable_data_hash = self._api_response["portable_data_hash"] self.set_committed(True) elif body: self._remember_api_response(self._my_api().collections().update( uuid=self._manifest_locator, body=body ).execute(num_retries=num_retries)) return self._manifest_text @must_be_writable @synchronized @retry_method def save_new(self, name=None, create_collection_record=True, owner_uuid=None, properties=None, storage_classes=None, trash_at=None, ensure_unique_name=False, num_retries=None, preserve_version=False): """Save collection to a new collection record. Commit pending buffer blocks to Keep and, when create_collection_record is True (default), create a new collection record. After creating a new collection record, this Collection object will be associated with the new record used by `save()`. Returns the current manifest text. :name: The collection name. :create_collection_record: If True, create a collection record on the API server. If False, only commit blocks to Keep and return the manifest text. :owner_uuid: the user, or project uuid that will own this collection. If None, defaults to the current user. :properties: Additional properties of collection. This value will replace any existing properties of collection. :storage_classes: Specify desirable storage classes to be used when writing data to Keep. :trash_at: A collection is *expiring* when it has a *trash_at* time in the future. An expiring collection can be accessed as normal, but is scheduled to be trashed automatically at the *trash_at* time. :ensure_unique_name: If True, ask the API server to rename the collection if it conflicts with a collection with the same name and owner. If False, a name conflict will result in an error. :num_retries: Retry count on API calls (if None, use the collection default) :preserve_version: If True, indicate that the collection content being saved right now should be preserved in a version snapshot if the collection record is updated in the future. Requires that the API server has Collections.CollectionVersioning enabled, if not, setting this will raise an exception. """ if properties and type(properties) is not dict: raise errors.ArgumentError("properties must be dictionary type.") if storage_classes and type(storage_classes) is not list: raise errors.ArgumentError("storage_classes must be list type.") if trash_at and type(trash_at) is not datetime.datetime: raise errors.ArgumentError("trash_at must be datetime type.") if preserve_version and not self._my_api().config()['Collections'].get('CollectionVersioning', False): raise errors.ArgumentError("preserve_version is not supported when CollectionVersioning is not enabled.") if self._has_remote_blocks: # Copy any remote blocks to the local cluster. self._copy_remote_blocks(remote_blocks={}) self._has_remote_blocks = False if storage_classes: self._storage_classes_desired = storage_classes self._my_block_manager().commit_all() text = self.manifest_text(strip=False) if create_collection_record: if name is None: name = "New collection" ensure_unique_name = True body = {"manifest_text": text, "name": name, "replication_desired": self.replication_desired} if owner_uuid: body["owner_uuid"] = owner_uuid if properties: body["properties"] = properties if self.storage_classes_desired(): body["storage_classes_desired"] = self.storage_classes_desired() if trash_at: t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ") body["trash_at"] = t if preserve_version: body["preserve_version"] = preserve_version self._remember_api_response(self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries)) text = self._api_response["manifest_text"] self._manifest_locator = self._api_response["uuid"] self._portable_data_hash = self._api_response["portable_data_hash"] self._manifest_text = text self.set_committed(True) return text _token_re = re.compile(r'(\S+)(\s+|$)') _block_re = re.compile(r'[0-9a-f]{32}\+(\d+)(\+\S+)*') _segment_re = re.compile(r'(\d+):(\d+):(\S+)') def _unescape_manifest_path(self, path): return re.sub('\\\\([0-3][0-7][0-7])', lambda m: chr(int(m.group(1), 8)), path) @synchronized def _import_manifest(self, manifest_text): """Import a manifest into a `Collection`. :manifest_text: The manifest text to import from. """ if len(self) > 0: raise ArgumentError("Can only import manifest into an empty collection") STREAM_NAME = 0 BLOCKS = 1 SEGMENTS = 2 stream_name = None state = STREAM_NAME for token_and_separator in self._token_re.finditer(manifest_text): tok = token_and_separator.group(1) sep = token_and_separator.group(2) if state == STREAM_NAME: # starting a new stream stream_name = self._unescape_manifest_path(tok) blocks = [] segments = [] streamoffset = 0 state = BLOCKS self.find_or_create(stream_name, COLLECTION) continue if state == BLOCKS: block_locator = self._block_re.match(tok) if block_locator: blocksize = int(block_locator.group(1)) blocks.append(Range(tok, streamoffset, blocksize, 0)) streamoffset += blocksize else: state = SEGMENTS if state == SEGMENTS: file_segment = self._segment_re.match(tok) if file_segment: pos = int(file_segment.group(1)) size = int(file_segment.group(2)) name = self._unescape_manifest_path(file_segment.group(3)) if name.split('/')[-1] == '.': # placeholder for persisting an empty directory, not a real file if len(name) > 2: self.find_or_create(os.path.join(stream_name, name[:-2]), COLLECTION) else: filepath = os.path.join(stream_name, name) try: afile = self.find_or_create(filepath, FILE) except IOError as e: if e.errno == errno.ENOTDIR: raise errors.SyntaxError("Dir part of %s conflicts with file of the same name.", filepath) from None else: raise e from None if isinstance(afile, ArvadosFile): afile.add_segment(blocks, pos, size) else: raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath) else: # error! raise errors.SyntaxError("Invalid manifest format, expected file segment but did not match format: '%s'" % tok) if sep == "\n": stream_name = None state = STREAM_NAME self.set_committed(True) @synchronized def notify(self, event, collection, name, item): if self._callback: self._callback(event, collection, name, item)Ancestors
Subclasses
Methods
def api_response(self)-
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.
def clone(self, new_parent=None, new_name=None, readonly=False, new_config=None)def find(self, path)def find_or_create(self, path, create_type)def get_properties(self)def get_trash_at(self)def known_past_version(self, modified_at_and_portable_data_hash)def manifest_locator(self)-
Get the manifest locator, if any.
The manifest locator will be set when the collection is loaded from an API server record or the portable data hash of a manifest.
The manifest locator will be None if the collection is newly created or was created directly from manifest text. The method
save_new()will assign a manifest locator. def notify(self, event, collection, name, item)def remove(self, path, recursive=False)def root_collection(self)def save(self, properties=None, storage_classes=None, trash_at=None, merge=True, num_retries=None, preserve_version=False)-
Save collection to an existing collection record.
Commit pending buffer blocks to Keep, merge with remote record (if merge=True, the default), and update the collection record. Returns the current manifest text.
Will raise AssertionError if not associated with a collection record on the API server. If you want to save a manifest to Keep only, see
save_new().:properties: Additional properties of collection. This value will replace any existing properties of collection.
:storage_classes: Specify desirable storage classes to be used when writing data to Keep.
:trash_at: A collection is expiring when it has a trash_at time in the future. An expiring collection can be accessed as normal, but is scheduled to be trashed automatically at the trash_at time.
:merge: Update and merge remote changes before saving. Otherwise, any remote changes will be ignored and overwritten.
:num_retries: Retry count on API calls (if None, use the collection default)
:preserve_version: If True, indicate that the collection content being saved right now should be preserved in a version snapshot if the collection record is updated in the future. Requires that the API server has Collections.CollectionVersioning enabled, if not, setting this will raise an exception.
def save_new(self, name=None, create_collection_record=True, owner_uuid=None, properties=None, storage_classes=None, trash_at=None, ensure_unique_name=False, num_retries=None, preserve_version=False)-
Save collection to a new collection record.
Commit pending buffer blocks to Keep and, when create_collection_record is True (default), create a new collection record. After creating a new collection record, this Collection object will be associated with the new record used by
save(). Returns the current manifest text.:name: The collection name.
:create_collection_record: If True, create a collection record on the API server. If False, only commit blocks to Keep and return the manifest text.
:owner_uuid: the user, or project uuid that will own this collection. If None, defaults to the current user.
:properties: Additional properties of collection. This value will replace any existing properties of collection.
:storage_classes: Specify desirable storage classes to be used when writing data to Keep.
:trash_at: A collection is expiring when it has a trash_at time in the future. An expiring collection can be accessed as normal, but is scheduled to be trashed automatically at the trash_at time.
:ensure_unique_name: If True, ask the API server to rename the collection if it conflicts with a collection with the same name and owner. If False, a name conflict will result in an error.
:num_retries: Retry count on API calls (if None, use the collection default)
:preserve_version: If True, indicate that the collection content being saved right now should be preserved in a version snapshot if the collection record is updated in the future. Requires that the API server has Collections.CollectionVersioning enabled, if not, setting this will raise an exception.
def stop_threads(self)def storage_classes_desired(self)def stream_name(self)def update(self, other=None, num_retries=None)-
Merge the latest collection on the API server with the current collection.
def writable(self)
Inherited members
class CollectionBase-
Abstract base class for Collection classes.
Expand source code
class CollectionBase(object): """Abstract base class for Collection classes.""" 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): """Get the manifest with locator hints stripped. 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(arvados.util.keep_locator_pattern, x) else x) for x in fields[1:]] clean += [' '.join(clean_fields), "\n"] return ''.join(clean)Subclasses
Methods
def stripped_manifest(self)-
Get the manifest with locator hints stripped.
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.
class CollectionReader (manifest_locator_or_text, *args, **kwargs)-
A read-only collection object.
Initialize from a collection UUID or portable data hash, or raw manifest text. See
Collectionconstructor for detailed options.Collection constructor.
:manifest_locator_or_text: An Arvados collection UUID, portable data hash, raw manifest text, or (if creating an empty collection) None.
:parent: the parent Collection, may be None.
:apiconfig: A dict containing keys for ARVADOS_API_HOST and ARVADOS_API_TOKEN. Prefer this over supplying your own api_client and keep_client (except in testing). Will use default config settings if not specified.
:api_client: The API client object to use for requests. If not specified, create one using
apiconfig.:keep_client: the Keep client to use for requests. If not specified, create one using
apiconfig.:num_retries: the number of retries for API and Keep requests.
:block_manager: the block manager to use. If not specified, create one.
:replication_desired: How many copies should Arvados maintain. If None, API server default configuration applies. If not None, this value will also be used for determining the number of block copies being written.
:storage_classes_desired: A list of storage class names where to upload the data. If None, the keep client is expected to store the data into the cluster's default storage class(es).
Expand source code
class CollectionReader(Collection): """A read-only collection object. Initialize from a collection UUID or portable data hash, or raw manifest text. See `Collection` constructor for detailed options. """ def __init__(self, manifest_locator_or_text, *args, **kwargs): self._in_init = True super(CollectionReader, self).__init__(manifest_locator_or_text, *args, **kwargs) self._in_init = False # Forego any locking since it should never change once initialized. self.lock = NoopLock() # Backwards compatability with old CollectionReader # all_streams() and all_files() self._streams = None def writable(self): return self._in_init def _populate_streams(orig_func): @functools.wraps(orig_func) def populate_streams_wrapper(self, *args, **kwargs): # Defer populating self._streams until needed since it creates a copy of the manifest. if self._streams is None: if self._manifest_text: self._streams = [sline.split() for sline in self._manifest_text.split("\n") if sline] else: self._streams = [] return orig_func(self, *args, **kwargs) return populate_streams_wrapper @_populate_streams def normalize(self): """Normalize the streams returned by `all_streams`. This method is kept for backwards compatability and only affects the behavior of `all_streams()` and `all_files()` """ # 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.locator, r.range_size)) self._streams = [normalize_stream(s, streams[s]) for s in sorted(streams)] @_populate_streams def all_streams(self): return [StreamReader(s, self._my_keep(), num_retries=self.num_retries) for s in self._streams] @_populate_streams def all_files(self): for s in self.all_streams(): for f in s.all_files(): yield fAncestors
Methods
def all_files(self)def all_streams(self)def normalize(self)-
Normalize the streams returned by
all_streams.This method is kept for backwards compatability and only affects the behavior of
all_streams()andall_files() def writable(self)
Inherited members
class CollectionWriter (api_client=None, num_retries=0, replication=None)-
Deprecated, use Collection instead.
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. * 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.
Expand source code
class CollectionWriter(CollectionBase): """Deprecated, use Collection instead.""" def __init__(self, api_client=None, num_retries=0, replication=None): """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. * 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 self._current_stream_files = [] self._current_stream_length = 0 self._current_stream_locators = [] self._current_stream_name = '.' self._current_file_name = None self._current_file_pos = 0 self._finished_streams = [] self._close_file = None self._queued_file = None self._queued_dirents = deque() self._queued_trees = deque() self._last_open = None 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: # * _queued_file: The file object we're currently writing to the # Collection. # * _queued_dirents: Entries under the current directory # (_queued_trees[0]) that we want to write or recurse through. # This may contain files from subdirectories if # max_manifest_depth == 0 for this directory. # * _queued_trees: Directories that should be written as separate # streams to the Collection. # This function handles the smallest piece of work currently queued # (current file, then current directory, then next directory) until # no work remains. The _work_THING methods each do a unit of work on # THING. _queue_THING methods add a THING to the work queue. while True: if self._queued_file: self._work_file() elif self._queued_dirents: self._work_dirents() elif self._queued_trees: self._work_trees() else: break def _work_file(self): while True: buf = self._queued_file.read(config.KEEP_BLOCK_SIZE) if not buf: break self.write(buf) self.finish_current_file() if self._close_file: self._queued_file.close() self._close_file = None self._queued_file = None def _work_dirents(self): path, stream_name, max_manifest_depth = self._queued_trees[0] if stream_name != self.current_stream_name(): self.start_new_stream(stream_name) while self._queued_dirents: dirent = self._queued_dirents.popleft() target = os.path.join(path, dirent) if os.path.isdir(target): self._queue_tree(target, os.path.join(stream_name, dirent), max_manifest_depth - 1) else: self._queue_file(target, dirent) break if not self._queued_dirents: self._queued_trees.popleft() def _work_trees(self): path, stream_name, max_manifest_depth = self._queued_trees[0] d = arvados.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() def _queue_file(self, source, filename=None): assert (self._queued_file is None), "tried to queue more than one file" if not hasattr(source, 'read'): source = open(source, 'rb') self._close_file = True else: self._close_file = False if filename is None: filename = os.path.basename(source.name) self.start_new_file(filename) self._queued_file = source def _queue_dirents(self, stream_name, dirents): assert (not self._queued_dirents), "tried to queue more than one tree" self._queued_dirents = deque(sorted(dirents)) def _queue_tree(self, path, stream_name, max_manifest_depth): self._queued_trees.append((path, stream_name, max_manifest_depth)) def write_file(self, source, filename=None): self._queue_file(source, filename) self.do_queued_work() def write_directory_tree(self, path, stream_name='.', max_manifest_depth=-1): self._queue_tree(path, stream_name, max_manifest_depth) self.do_queued_work() def write(self, newdata): if isinstance(newdata, bytes): pass elif isinstance(newdata, str): newdata = newdata.encode() elif hasattr(newdata, '__iter__'): for s in newdata: self.write(s) return self._data_buffer.append(newdata) self._data_buffer_len += len(newdata) self._current_stream_length += len(newdata) while self._data_buffer_len >= config.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( u"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 = b''.join(self._data_buffer) if data_buffer: self._current_stream_locators.append( self._my_keep().put( data_buffer[0:config.KEEP_BLOCK_SIZE], copies=self.replication)) self._data_buffer = [data_buffer[config.KEEP_BLOCK_SIZE:]] self._data_buffer_len = len(self._data_buffer[0]) def start_new_file(self, newfilename=None): self.finish_current_file() self.set_current_file_name(newfilename) def set_current_file_name(self, newfilename): if re.search(r'[\t\n]', newfilename): 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 is None: if self._current_file_pos == self._current_stream_length: return raise errors.AssertionError( "Cannot finish an unnamed file " + "(%d bytes at offset %d in '%s' stream)" % (self._current_stream_length - self._current_file_pos, self._current_file_pos, self._current_stream_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() self.set_current_stream_name(newstreamname) def set_current_stream_name(self, newstreamname): if re.search(r'[\t\n]', newstreamname): raise errors.AssertionError( "Manifest stream names cannot contain whitespace: '%s'" % (newstreamname)) self._current_stream_name = '.' if newstreamname=='' else newstreamname def current_stream_name(self): return self._current_stream_name def finish_current_stream(self): self.finish_current_file() self.flush_data() if not self._current_stream_files: pass 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 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 = [] self._current_stream_name = None self._current_file_pos = 0 self._current_file_name = None def finish(self): """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().encode(), copies=self.replication) def portable_data_hash(self): stripped = self.stripped_manifest().encode() return '{}+{}'.format(hashlib.md5(stripped).hexdigest(), len(stripped)) def manifest_text(self): self.finish_current_stream() manifest = '' for stream in self._finished_streams: if not re.search(r'^\.(/.*)?$', stream[0]): manifest += './' manifest += stream[0].replace(' ', '\\040') manifest += ' ' + ' '.join(stream[1]) manifest += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2]) manifest += "\n" return manifest def data_locators(self): ret = [] for name, locators, files in self._finished_streams: ret += locators return ret def save_new(self, name=None): return self._api_client.collections().create( ensure_unique_name=True, body={ 'name': name, 'manifest_text': self.manifest_text(), }).execute(num_retries=self.num_retries)Ancestors
Subclasses
Methods
def current_file_name(self)def current_stream_name(self)def data_locators(self)def do_queued_work(self)def finish(self)-
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.
def finish_current_file(self)def finish_current_stream(self)def flush_data(self)def manifest_text(self)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)
def portable_data_hash(self)def save_new(self, name=None)def set_current_file_name(self, newfilename)def set_current_stream_name(self, newstreamname)def start_new_file(self, newfilename=None)def start_new_stream(self, newstreamname='.')def write(self, newdata)def write_directory_tree(self, path, stream_name='.', max_manifest_depth=-1)def write_file(self, source, filename=None)
Inherited members
class ResumableCollectionWriter (api_client=None, **kwargs)-
Deprecated, use Collection instead.
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. * 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.
Expand source code
class ResumableCollectionWriter(CollectionWriter): """Deprecated, use Collection instead.""" STATE_PROPS = ['_current_stream_files', '_current_stream_length', '_current_stream_locators', '_current_stream_name', '_current_file_name', '_current_file_pos', '_close_file', '_data_buffer', '_dependencies', '_finished_streams', '_queued_dirents', '_queued_trees'] def __init__(self, api_client=None, **kwargs): self._dependencies = {} super(ResumableCollectionWriter, self).__init__(api_client, **kwargs) @classmethod def from_state(cls, state, *init_args, **init_kwargs): # Try to build a new writer from scratch with the given state. # If the state is not suitable to resume (because files have changed, # been deleted, aren't predictable, etc.), raise a # StaleWriterStateError. Otherwise, return the initialized writer. # The caller is responsible for calling writer.do_queued_work() # appropriately after it's returned. writer = cls(*init_args, **init_kwargs) for attr_name in cls.STATE_PROPS: attr_value = state[attr_name] attr_class = getattr(writer, attr_name).__class__ # Coerce the value into the same type as the initial value, if # needed. if attr_class not in (type(None), attr_value.__class__): attr_value = attr_class(attr_value) setattr(writer, attr_name, attr_value) # Check dependencies before we try to resume anything. if any(KeepLocator(ls).permission_expired() for ls in writer._current_stream_locators): raise errors.StaleWriterStateError( "locators include expired permission hint") writer.check_dependencies() if state['_current_file'] is not None: path, pos = state['_current_file'] try: writer._queued_file = open(path, 'rb') writer._queued_file.seek(pos) except IOError as error: raise errors.StaleWriterStateError( u"failed to reopen active file {}: {}".format(path, error)) return writer def check_dependencies(self): for path, orig_stat in listitems(self._dependencies): if not S_ISREG(orig_stat[ST_MODE]): raise errors.StaleWriterStateError(u"{} not file".format(path)) try: now_stat = tuple(os.stat(path)) except OSError as error: raise errors.StaleWriterStateError( u"failed to stat {}: {}".format(path, error)) if ((not S_ISREG(now_stat[ST_MODE])) or (orig_stat[ST_MTIME] != now_stat[ST_MTIME]) or (orig_stat[ST_SIZE] != now_stat[ST_SIZE])): raise errors.StaleWriterStateError(u"{} changed".format(path)) def dump_state(self, copy_func=lambda x: x): state = {attr: copy_func(getattr(self, attr)) for attr in self.STATE_PROPS} if self._queued_file is None: state['_current_file'] = None else: state['_current_file'] = (os.path.realpath(self._queued_file.name), self._queued_file.tell()) return state def _queue_file(self, source, filename=None): try: src_path = os.path.realpath(source) except Exception: raise errors.AssertionError(u"{} not a file path".format(source)) try: path_stat = os.stat(src_path) except OSError as stat_error: path_stat = None super(ResumableCollectionWriter, self)._queue_file(source, filename) fd_stat = os.fstat(self._queued_file.fileno()) if not S_ISREG(fd_stat.st_mode): # We won't be able to resume from this cache anyway, so don't # worry about further checks. self._dependencies[source] = tuple(fd_stat) elif path_stat is None: raise errors.AssertionError( u"could not stat {}: {}".format(source, stat_error)) elif path_stat.st_ino != fd_stat.st_ino: raise errors.AssertionError( u"{} changed between open and stat calls".format(source)) else: self._dependencies[src_path] = tuple(fd_stat) def write(self, data): if self._queued_file is None: raise errors.AssertionError( "resumable writer can't accept unsourced data") return super(ResumableCollectionWriter, self).write(data)Ancestors
Class variables
var STATE_PROPS
Static methods
def from_state(state, *init_args, **init_kwargs)
Methods
def check_dependencies(self)def dump_state(self, copy_func=<function ResumableCollectionWriter.<lambda>>)def write(self, data)
Inherited members
class RichCollectionBase (parent=None)-
Base class for Collections and Subcollections.
Implements the majority of functionality relating to accessing items in the Collection.
Expand source code
class RichCollectionBase(CollectionBase): """Base class for Collections and Subcollections. Implements the majority of functionality relating to accessing items in the Collection. """ def __init__(self, parent=None): self.parent = parent self._committed = False self._has_remote_blocks = False self._callback = None self._items = {} def _my_api(self): raise NotImplementedError() def _my_keep(self): raise NotImplementedError() def _my_block_manager(self): raise NotImplementedError() def writable(self): raise NotImplementedError() def root_collection(self): raise NotImplementedError() def notify(self, event, collection, name, item): raise NotImplementedError() def stream_name(self): raise NotImplementedError() @synchronized def has_remote_blocks(self): """Recursively check for a +R segment locator signature.""" if self._has_remote_blocks: return True for item in self: if self[item].has_remote_blocks(): return True return False @synchronized def set_has_remote_blocks(self, val): self._has_remote_blocks = val if self.parent: self.parent.set_has_remote_blocks(val) @must_be_writable @synchronized def find_or_create(self, path, create_type): """Recursively search the specified file path. May return either a `Collection` or `ArvadosFile`. If not found, will create a new item at the specified path based on `create_type`. Will create intermediate subcollections needed to contain the final item in the path. :create_type: One of `arvados.collection.FILE` or `arvados.collection.COLLECTION`. If the path is not found, and value of create_type is FILE then create and return a new ArvadosFile for the last path component. If COLLECTION, then create and return a new Collection for the last path component. """ pathcomponents = path.split("/", 1) if pathcomponents[0]: item = self._items.get(pathcomponents[0]) if len(pathcomponents) == 1: if item is None: # create new file if create_type == COLLECTION: item = Subcollection(self, pathcomponents[0]) else: item = ArvadosFile(self, pathcomponents[0]) self._items[pathcomponents[0]] = item self.set_committed(False) self.notify(ADD, self, pathcomponents[0], item) return item else: if item is None: # create new collection item = Subcollection(self, pathcomponents[0]) self._items[pathcomponents[0]] = item self.set_committed(False) self.notify(ADD, self, pathcomponents[0], item) if isinstance(item, RichCollectionBase): return item.find_or_create(pathcomponents[1], create_type) else: raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0]) else: return self @synchronized def find(self, path): """Recursively search the specified file path. May return either a Collection or ArvadosFile. Return None if not found. If path is invalid (ex: starts with '/'), an IOError exception will be raised. """ if not path: raise errors.ArgumentError("Parameter 'path' is empty.") pathcomponents = path.split("/", 1) if pathcomponents[0] == '': raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0]) item = self._items.get(pathcomponents[0]) if item is None: return None elif len(pathcomponents) == 1: return item else: if isinstance(item, RichCollectionBase): if pathcomponents[1]: return item.find(pathcomponents[1]) else: return item else: raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0]) @synchronized def mkdirs(self, path): """Recursive subcollection create. Like `os.makedirs()`. Will create intermediate subcollections needed to contain the leaf subcollection path. """ if self.find(path) != None: raise IOError(errno.EEXIST, "Directory or file exists", path) return self.find_or_create(path, COLLECTION) def open(self, path, mode="r", encoding=None): """Open a file-like object for access. :path: path to a file in the collection :mode: a string consisting of "r", "w", or "a", optionally followed by "b" or "t", optionally followed by "+". :"b": binary mode: write() accepts bytes, read() returns bytes. :"t": text mode (default): write() accepts strings, read() returns strings. :"r": opens for reading :"r+": opens for reading and writing. Reads/writes share a file pointer. :"w", "w+": truncates to 0 and opens for reading and writing. Reads/writes share a file pointer. :"a", "a+": opens for reading and writing. All writes are appended to the end of the file. Writing does not affect the file pointer for reading. """ if not re.search(r'^[rwa][bt]?\+?$', mode): raise errors.ArgumentError("Invalid mode {!r}".format(mode)) if mode[0] == 'r' and '+' not in mode: fclass = ArvadosFileReader arvfile = self.find(path) elif not self.writable(): raise IOError(errno.EROFS, "Collection is read only") else: fclass = ArvadosFileWriter arvfile = self.find_or_create(path, FILE) if arvfile is None: raise IOError(errno.ENOENT, "File not found", path) if not isinstance(arvfile, ArvadosFile): raise IOError(errno.EISDIR, "Is a directory", path) if mode[0] == 'w': arvfile.truncate(0) binmode = mode[0] + 'b' + re.sub('[bt]', '', mode[1:]) f = fclass(arvfile, mode=binmode, num_retries=self.num_retries) if 'b' not in mode: bufferclass = io.BufferedRandom if f.writable() else io.BufferedReader f = TextIOWrapper(bufferclass(WrappableFile(f)), encoding=encoding) return f def modified(self): """Determine if the collection has been modified since last commited.""" return not self.committed() @synchronized def committed(self): """Determine if the collection has been committed to the API server.""" return self._committed @synchronized def set_committed(self, value=True): """Recursively set committed flag. If value is True, set committed to be True for this and all children. If value is False, set committed to be False for this and all parents. """ if value == self._committed: return if value: for k,v in listitems(self._items): v.set_committed(True) self._committed = True else: self._committed = False if self.parent is not None: self.parent.set_committed(False) @synchronized def __iter__(self): """Iterate over names of files and collections contained in this collection.""" return iter(viewkeys(self._items)) @synchronized def __getitem__(self, k): """Get a file or collection that is directly contained by this collection. If you want to search a path, use `find()` instead. """ return self._items[k] @synchronized def __contains__(self, k): """Test if there is a file or collection a directly contained by this collection.""" return k in self._items @synchronized def __len__(self): """Get the number of items directly contained in this collection.""" return len(self._items) @must_be_writable @synchronized def __delitem__(self, p): """Delete an item by name which is directly contained by this collection.""" del self._items[p] self.set_committed(False) self.notify(DEL, self, p, None) @synchronized def keys(self): """Get a list of names of files and collections directly contained in this collection.""" return self._items.keys() @synchronized def values(self): """Get a list of files and collection objects directly contained in this collection.""" return listvalues(self._items) @synchronized def items(self): """Get a list of (name, object) tuples directly contained in this collection.""" return listitems(self._items) def exists(self, path): """Test if there is a file or collection at `path`.""" return self.find(path) is not None @must_be_writable @synchronized def remove(self, path, recursive=False): """Remove the file or subcollection (directory) at `path`. :recursive: Specify whether to remove non-empty subcollections (True), or raise an error (False). """ if not path: raise errors.ArgumentError("Parameter 'path' is empty.") pathcomponents = path.split("/", 1) item = self._items.get(pathcomponents[0]) if item is None: raise IOError(errno.ENOENT, "File not found", path) if len(pathcomponents) == 1: if isinstance(self._items[pathcomponents[0]], RichCollectionBase) and len(self._items[pathcomponents[0]]) > 0 and not recursive: raise IOError(errno.ENOTEMPTY, "Directory not empty", path) deleteditem = self._items[pathcomponents[0]] del self._items[pathcomponents[0]] self.set_committed(False) self.notify(DEL, self, pathcomponents[0], deleteditem) else: item.remove(pathcomponents[1], recursive=recursive) def _clonefrom(self, source): for k,v in listitems(source): self._items[k] = v.clone(self, k) def clone(self): raise NotImplementedError() @must_be_writable @synchronized def add(self, source_obj, target_name, overwrite=False, reparent=False): """Copy or move a file or subcollection to this collection. :source_obj: An ArvadosFile, or Subcollection object :target_name: Destination item name. If the target name already exists and is a file, this will raise an error unless you specify `overwrite=True`. :overwrite: Whether to overwrite target file if it already exists. :reparent: If True, source_obj will be moved from its parent collection to this collection. If False, source_obj will be copied and the parent collection will be unmodified. """ if target_name in self and not overwrite: raise IOError(errno.EEXIST, "File already exists", target_name) modified_from = None if target_name in self: modified_from = self[target_name] # Actually make the move or copy. if reparent: source_obj._reparent(self, target_name) item = source_obj else: item = source_obj.clone(self, target_name) self._items[target_name] = item self.set_committed(False) if not self._has_remote_blocks and source_obj.has_remote_blocks(): self.set_has_remote_blocks(True) if modified_from: self.notify(MOD, self, target_name, (modified_from, item)) else: self.notify(ADD, self, target_name, item) def _get_src_target(self, source, target_path, source_collection, create_dest): if source_collection is None: source_collection = self # Find the object if isinstance(source, basestring): source_obj = source_collection.find(source) if source_obj is None: raise IOError(errno.ENOENT, "File not found", source) sourcecomponents = source.split("/") else: source_obj = source sourcecomponents = None # Find parent collection the target path targetcomponents = target_path.split("/") # Determine the name to use. target_name = targetcomponents[-1] if targetcomponents[-1] else sourcecomponents[-1] if not target_name: raise errors.ArgumentError("Target path is empty and source is an object. Cannot determine destination filename to use.") if create_dest: target_dir = self.find_or_create("/".join(targetcomponents[0:-1]), COLLECTION) else: if len(targetcomponents) > 1: target_dir = self.find("/".join(targetcomponents[0:-1])) else: target_dir = self if target_dir is None: raise IOError(errno.ENOENT, "Target directory not found", target_name) if target_name in target_dir and isinstance(target_dir[target_name], RichCollectionBase) and sourcecomponents: target_dir = target_dir[target_name] target_name = sourcecomponents[-1] return (source_obj, target_dir, target_name) @must_be_writable @synchronized def copy(self, source, target_path, source_collection=None, overwrite=False): """Copy a file or subcollection to a new path in this collection. :source: A string with a path to source file or subcollection, or an actual ArvadosFile or Subcollection object. :target_path: Destination file or path. If the target path already exists and is a subcollection, the item will be placed inside the subcollection. If the target path already exists and is a file, this will raise an error unless you specify `overwrite=True`. :source_collection: Collection to copy `source_path` from (default `self`) :overwrite: Whether to overwrite target file if it already exists. """ source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, True) target_dir.add(source_obj, target_name, overwrite, False) @must_be_writable @synchronized def rename(self, source, target_path, source_collection=None, overwrite=False): """Move a file or subcollection from `source_collection` to a new path in this collection. :source: A string with a path to source file or subcollection. :target_path: Destination file or path. If the target path already exists and is a subcollection, the item will be placed inside the subcollection. If the target path already exists and is a file, this will raise an error unless you specify `overwrite=True`. :source_collection: Collection to copy `source_path` from (default `self`) :overwrite: Whether to overwrite target file if it already exists. """ source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, False) if not source_obj.writable(): raise IOError(errno.EROFS, "Source collection is read only", source) target_dir.add(source_obj, target_name, overwrite, True) def portable_manifest_text(self, stream_name="."): """Get the manifest text for this collection, sub collections and files. This method does not flush outstanding blocks to Keep. It will return a normalized manifest with access tokens stripped. :stream_name: Name to use for this stream (directory) """ return self._get_manifest_text(stream_name, True, True) @synchronized def manifest_text(self, stream_name=".", strip=False, normalize=False, only_committed=False): """Get the manifest text for this collection, sub collections and files. This method will flush outstanding blocks to Keep. By default, it will not normalize an unmodified manifest or strip access tokens. :stream_name: Name to use for this stream (directory) :strip: If True, remove signing tokens from block locators if present. If False (default), block locators are left unchanged. :normalize: If True, always export the manifest text in normalized form even if the Collection is not modified. If False (default) and the collection is not modified, return the original manifest text even if it is not in normalized form. :only_committed: If True, don't commit pending blocks. """ if not only_committed: self._my_block_manager().commit_all() return self._get_manifest_text(stream_name, strip, normalize, only_committed=only_committed) @synchronized def _get_manifest_text(self, stream_name, strip, normalize, only_committed=False): """Get the manifest text for this collection, sub collections and files. :stream_name: Name to use for this stream (directory) :strip: If True, remove signing tokens from block locators if present. If False (default), block locators are left unchanged. :normalize: If True, always export the manifest text in normalized form even if the Collection is not modified. If False (default) and the collection is not modified, return the original manifest text even if it is not in normalized form. :only_committed: If True, only include blocks that were already committed to Keep. """ if not self.committed() or self._manifest_text is None or normalize: stream = {} buf = [] sorted_keys = sorted(self.keys()) for filename in [s for s in sorted_keys if isinstance(self[s], ArvadosFile)]: # Create a stream per file `k` arvfile = self[filename] filestream = [] for segment in arvfile.segments(): loc = segment.locator if arvfile.parent._my_block_manager().is_bufferblock(loc): if only_committed: continue loc = arvfile.parent._my_block_manager().get_bufferblock(loc).locator() if strip: loc = KeepLocator(loc).stripped() filestream.append(LocatorAndRange(loc, KeepLocator(loc).size, segment.segment_offset, segment.range_size)) stream[filename] = filestream if stream: buf.append(" ".join(normalize_stream(stream_name, stream)) + "\n") for dirname in [s for s in sorted_keys if isinstance(self[s], RichCollectionBase)]: buf.append(self[dirname].manifest_text( stream_name=os.path.join(stream_name, dirname), strip=strip, normalize=True, only_committed=only_committed)) return "".join(buf) else: if strip: return self.stripped_manifest() else: return self._manifest_text @synchronized def _copy_remote_blocks(self, remote_blocks={}): """Scan through the entire collection and ask Keep to copy remote blocks. When accessing a remote collection, blocks will have a remote signature (+R instead of +A). Collect these signatures and request Keep to copy the blocks to the local cluster, returning local (+A) signatures. :remote_blocks: Shared cache of remote to local block mappings. This is used to avoid doing extra work when blocks are shared by more than one file in different subdirectories. """ for item in self: remote_blocks = self[item]._copy_remote_blocks(remote_blocks) return remote_blocks @synchronized def diff(self, end_collection, prefix=".", holding_collection=None): """Generate list of add/modify/delete actions. When given to `apply`, will change `self` to match `end_collection` """ changes = [] if holding_collection is None: holding_collection = Collection(api_client=self._my_api(), keep_client=self._my_keep()) for k in self: if k not in end_collection: changes.append((DEL, os.path.join(prefix, k), self[k].clone(holding_collection, ""))) for k in end_collection: if k in self: if isinstance(end_collection[k], Subcollection) and isinstance(self[k], Subcollection): changes.extend(self[k].diff(end_collection[k], os.path.join(prefix, k), holding_collection)) elif end_collection[k] != self[k]: changes.append((MOD, os.path.join(prefix, k), self[k].clone(holding_collection, ""), end_collection[k].clone(holding_collection, ""))) else: changes.append((TOK, os.path.join(prefix, k), self[k].clone(holding_collection, ""), end_collection[k].clone(holding_collection, ""))) else: changes.append((ADD, os.path.join(prefix, k), end_collection[k].clone(holding_collection, ""))) return changes @must_be_writable @synchronized def apply(self, changes): """Apply changes from `diff`. If a change conflicts with a local change, it will be saved to an alternate path indicating the conflict. """ if changes: self.set_committed(False) for change in changes: event_type = change[0] path = change[1] initial = change[2] local = self.find(path) conflictpath = "%s~%s~conflict~" % (path, time.strftime("%Y%m%d-%H%M%S", time.gmtime())) if event_type == ADD: if local is None: # No local file at path, safe to copy over new file self.copy(initial, path) elif local is not None and local != initial: # There is already local file and it is different: # save change to conflict file. self.copy(initial, conflictpath) elif event_type == MOD or event_type == TOK: final = change[3] if local == initial: # Local matches the "initial" item so it has not # changed locally and is safe to update. if isinstance(local, ArvadosFile) and isinstance(final, ArvadosFile): # Replace contents of local file with new contents local.replace_contents(final) else: # Overwrite path with new item; this can happen if # path was a file and is now a collection or vice versa self.copy(final, path, overwrite=True) else: # Local is missing (presumably deleted) or local doesn't # match the "start" value, so save change to conflict file self.copy(final, conflictpath) elif event_type == DEL: if local == initial: # Local item matches "initial" value, so it is safe to remove. self.remove(path, recursive=True) # else, the file is modified or already removed, in either # case we don't want to try to remove it. def portable_data_hash(self): """Get the portable data hash for this collection's manifest.""" if self._manifest_locator and self.committed(): # If the collection is already saved on the API server, and it's committed # then return API server's PDH response. return self._portable_data_hash else: stripped = self.portable_manifest_text().encode() return '{}+{}'.format(hashlib.md5(stripped).hexdigest(), len(stripped)) @synchronized def subscribe(self, callback): if self._callback is None: self._callback = callback else: raise errors.ArgumentError("A callback is already set on this collection.") @synchronized def unsubscribe(self): if self._callback is not None: self._callback = None @synchronized def notify(self, event, collection, name, item): if self._callback: self._callback(event, collection, name, item) self.root_collection().notify(event, collection, name, item) @synchronized def __eq__(self, other): if other is self: return True if not isinstance(other, RichCollectionBase): return False if len(self._items) != len(other): return False for k in self._items: if k not in other: return False if self._items[k] != other[k]: return False return True def __ne__(self, other): return not self.__eq__(other) @synchronized def flush(self): """Flush bufferblocks to Keep.""" for e in listvalues(self): e.flush()Ancestors
Subclasses
Methods
def add(self, source_obj, target_name, overwrite=False, reparent=False)-
Copy or move a file or subcollection to this collection.
:source_obj: An ArvadosFile, or Subcollection object
:target_name: Destination item name. If the target name already exists and is a file, this will raise an error unless you specify
overwrite=True.:overwrite: Whether to overwrite target file if it already exists.
:reparent: If True, source_obj will be moved from its parent collection to this collection. If False, source_obj will be copied and the parent collection will be unmodified.
def apply(self, changes)-
Apply changes from
diff.If a change conflicts with a local change, it will be saved to an alternate path indicating the conflict.
def clone(self)def committed(self)-
Determine if the collection has been committed to the API server.
def copy(self, source, target_path, source_collection=None, overwrite=False)-
Copy a file or subcollection to a new path in this collection.
:source: A string with a path to source file or subcollection, or an actual ArvadosFile or Subcollection object.
:target_path: Destination file or path. If the target path already exists and is a subcollection, the item will be placed inside the subcollection. If the target path already exists and is a file, this will raise an error unless you specify
overwrite=True.:source_collection: Collection to copy
source_pathfrom (defaultself):overwrite: Whether to overwrite target file if it already exists.
def diff(self, end_collection, prefix='.', holding_collection=None)-
Generate list of add/modify/delete actions.
When given to
apply, will changeselfto matchend_collection def exists(self, path)-
Test if there is a file or collection at
path. def find(self, path)-
Recursively search the specified file path.
May return either a Collection or ArvadosFile. Return None if not found. If path is invalid (ex: starts with '/'), an IOError exception will be raised.
def find_or_create(self, path, create_type)-
Recursively search the specified file path.
May return either a
CollectionorArvadosFile. If not found, will create a new item at the specified path based oncreate_type. Will create intermediate subcollections needed to contain the final item in the path.:create_type: One of
arvados.collection.FILEorarvados.collection.COLLECTION. If the path is not found, and value of create_type is FILE then create and return a new ArvadosFile for the last path component. If COLLECTION, then create and return a new Collection for the last path component. def flush(self)-
Flush bufferblocks to Keep.
def has_remote_blocks(self)-
Recursively check for a +R segment locator signature.
def items(self)-
Get a list of (name, object) tuples directly contained in this collection.
def keys(self)-
Get a list of names of files and collections directly contained in this collection.
def manifest_text(self, stream_name='.', strip=False, normalize=False, only_committed=False)-
Get the manifest text for this collection, sub collections and files.
This method will flush outstanding blocks to Keep. By default, it will not normalize an unmodified manifest or strip access tokens.
:stream_name: Name to use for this stream (directory)
:strip: If True, remove signing tokens from block locators if present. If False (default), block locators are left unchanged.
:normalize: If True, always export the manifest text in normalized form even if the Collection is not modified. If False (default) and the collection is not modified, return the original manifest text even if it is not in normalized form.
:only_committed: If True, don't commit pending blocks.
def mkdirs(self, path)-
Recursive subcollection create.
Like
os.makedirs(). Will create intermediate subcollections needed to contain the leaf subcollection path. def modified(self)-
Determine if the collection has been modified since last commited.
def notify(self, event, collection, name, item)def open(self, path, mode='r', encoding=None)-
Open a file-like object for access.
:path: path to a file in the collection :mode: a string consisting of "r", "w", or "a", optionally followed by "b" or "t", optionally followed by "+". :"b": binary mode: write() accepts bytes, read() returns bytes. :"t": text mode (default): write() accepts strings, read() returns strings. :"r": opens for reading :"r+": opens for reading and writing. Reads/writes share a file pointer. :"w", "w+": truncates to 0 and opens for reading and writing. Reads/writes share a file pointer. :"a", "a+": opens for reading and writing. All writes are appended to the end of the file. Writing does not affect the file pointer for reading.
def portable_data_hash(self)-
Get the portable data hash for this collection's manifest.
def portable_manifest_text(self, stream_name='.')-
Get the manifest text for this collection, sub collections and files.
This method does not flush outstanding blocks to Keep. It will return a normalized manifest with access tokens stripped.
:stream_name: Name to use for this stream (directory)
def remove(self, path, recursive=False)-
Remove the file or subcollection (directory) at
path.:recursive: Specify whether to remove non-empty subcollections (True), or raise an error (False).
def rename(self, source, target_path, source_collection=None, overwrite=False)-
Move a file or subcollection from
source_collectionto a new path in this collection.:source: A string with a path to source file or subcollection.
:target_path: Destination file or path. If the target path already exists and is a subcollection, the item will be placed inside the subcollection. If the target path already exists and is a file, this will raise an error unless you specify
overwrite=True.:source_collection: Collection to copy
source_pathfrom (defaultself):overwrite: Whether to overwrite target file if it already exists.
def root_collection(self)def set_committed(self, value=True)-
Recursively set committed flag.
If value is True, set committed to be True for this and all children.
If value is False, set committed to be False for this and all parents.
def set_has_remote_blocks(self, val)def stream_name(self)def subscribe(self, callback)def unsubscribe(self)def values(self)-
Get a list of files and collection objects directly contained in this collection.
def writable(self)
Inherited members
class Subcollection (parent, name)-
This is a subdirectory within a collection that doesn't have its own API server record.
Subcollection locking falls under the umbrella lock of its root collection.
Expand source code
class Subcollection(RichCollectionBase): """This is a subdirectory within a collection that doesn't have its own API server record. Subcollection locking falls under the umbrella lock of its root collection. """ def __init__(self, parent, name): super(Subcollection, self).__init__(parent) self.lock = self.root_collection().lock self._manifest_text = None self.name = name self.num_retries = parent.num_retries def root_collection(self): return self.parent.root_collection() def writable(self): return self.root_collection().writable() def _my_api(self): return self.root_collection()._my_api() def _my_keep(self): return self.root_collection()._my_keep() def _my_block_manager(self): return self.root_collection()._my_block_manager() def stream_name(self): return os.path.join(self.parent.stream_name(), self.name) @synchronized def clone(self, new_parent, new_name): c = Subcollection(new_parent, new_name) c._clonefrom(self) return c @must_be_writable @synchronized def _reparent(self, newparent, newname): self.set_committed(False) self.flush() self.parent.remove(self.name, recursive=True) self.parent = newparent self.name = newname self.lock = self.parent.root_collection().lock @synchronized def _get_manifest_text(self, stream_name, strip, normalize, only_committed=False): """Encode empty directories by using an \056-named (".") empty file""" if len(self._items) == 0: return "%s %s 0:0:\\056\n" % ( escape(stream_name), config.EMPTY_BLOCK_LOCATOR) return super(Subcollection, self)._get_manifest_text(stream_name, strip, normalize, only_committed)Ancestors
Methods
def clone(self, new_parent, new_name)def root_collection(self)def stream_name(self)def writable(self)
Inherited members