import os
import re
import errno
+import time
from collections import deque
from stat import *
-from .arvfile import ArvadosFileBase, split, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, BlockManager
+from .arvfile import ArvadosFileBase, split, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, BlockManager, _synchronized, _must_be_writable, SYNC_READONLY, SYNC_EXPLICIT, SYNC_LIVE, NoopLock
from keep import *
from .stream import StreamReader, normalize_stream, locator_block_size
from .ranges import Range, LocatorAndRange
+from .safeapi import SafeApi
import config
import errors
import util
+import events
_logger = logging.getLogger('arvados.collection')
"resumable writer can't accept unsourced data")
return super(ResumableCollectionWriter, self).write(data)
+ADD = "add"
+DEL = "del"
-class Collection(CollectionBase):
- def __init__(self, manifest_locator_or_text=None, parent=None, api_client=None,
- keep_client=None, num_retries=0, block_manager=None):
-
+class SynchronizedCollectionBase(CollectionBase):
+ def __init__(self, parent=None):
self.parent = parent
- self._items = None
- self._api_client = api_client
- self._keep_client = keep_client
- self._block_manager = block_manager
-
- self.num_retries = num_retries
- self._manifest_locator = None
- self._manifest_text = None
- self._api_response = None
-
- if manifest_locator_or_text:
- if re.match(util.keep_locator_pattern, manifest_locator_or_text):
- self._manifest_locator = manifest_locator_or_text
- elif re.match(util.collection_uuid_pattern, manifest_locator_or_text):
- self._manifest_locator = manifest_locator_or_text
- elif re.match(util.manifest_pattern, manifest_locator_or_text):
- self._manifest_text = manifest_locator_or_text
- else:
- raise errors.ArgumentError(
- "Argument to CollectionReader must be a manifest or a collection UUID")
+ self._items = {}
def _my_api(self):
- if self._api_client is None:
- if self.parent is not None:
- return self.parent._my_api()
- self._api_client = arvados.api('v1')
- self._keep_client = None # Make a new one with the new api.
- return self._api_client
+ raise NotImplementedError()
def _my_keep(self):
- if self._keep_client is None:
- if self.parent is not None:
- return self.parent._my_keep()
- self._keep_client = KeepClient(api_client=self._my_api(),
- num_retries=self.num_retries)
- return self._keep_client
+ raise NotImplementedError()
def _my_block_manager(self):
- if self._block_manager is None:
- if self.parent is not None:
- return self.parent._my_block_manager()
- self._block_manager = BlockManager(self._my_keep())
- return self._block_manager
-
- def _populate_from_api_server(self):
- # As in KeepClient itself, we must wait until the last
- # possible moment to instantiate an API client, in order to
- # avoid tripping up clients that don't have access to an API
- # server. If we do build one, make sure our Keep client uses
- # it. If instantiation fails, we'll fall back to the except
- # clause, just like any other Collection lookup
- # failure. Return an exception, or None if successful.
- try:
- self._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']
- return None
- except Exception as e:
- return e
+ raise NotImplementedError()
- def _populate_from_keep(self):
- # Retrieve a manifest directly from Keep. This has a chance of
- # working if [a] the locator includes a permission signature
- # or [b] the Keep services are operating in world-readable
- # mode. Return an exception, or None if successful.
- try:
- self._manifest_text = self._my_keep().get(
- self._manifest_locator, num_retries=self.num_retries)
- except Exception as e:
- return e
+ def _root_lock(self):
+ raise NotImplementedError()
def _populate(self):
- self._items = {}
- if self._manifest_locator is None and self._manifest_text is None:
- return
- error_via_api = None
- error_via_keep = None
- should_try_keep = ((self._manifest_text is None) and
- util.keep_locator_pattern.match(
- self._manifest_locator))
- if ((self._manifest_text is None) and
- util.signed_locator_pattern.match(self._manifest_locator)):
- error_via_keep = self._populate_from_keep()
- if self._manifest_text is None:
- error_via_api = self._populate_from_api_server()
- if error_via_api is not None and not should_try_keep:
- raise error_via_api
- if ((self._manifest_text is None) and
- not error_via_keep and
- should_try_keep):
- # Looks like a keep locator, and we didn't already try keep above
- error_via_keep = self._populate_from_keep()
- if self._manifest_text is None:
- # Nothing worked!
- raise arvados.errors.NotFoundError(
- ("Failed to retrieve collection '{}' " +
- "from either API server ({}) or Keep ({})."
- ).format(
- self._manifest_locator,
- error_via_api,
- error_via_keep))
- # populate
- import_manifest(self._manifest_text, self)
-
- def _populate_first(orig_func):
- # Decorator for methods that read actual Collection data.
- @functools.wraps(orig_func)
- def wrapper(self, *args, **kwargs):
- if self._items is None:
- self._populate()
- return orig_func(self, *args, **kwargs)
- return wrapper
+ raise NotImplementedError()
- def __enter__(self):
- return self
+ def sync_mode(self):
+ raise NotImplementedError()
- def __exit__(self, exc_type, exc_value, traceback):
- self.save(no_locator=True)
- if self._block_manager is not None:
- self._block_manager.stop_threads()
+ def notify(self, collection, event, name, item):
+ raise NotImplementedError()
- @_populate_first
+ @_synchronized
def find(self, path, create=False, create_collection=False):
+ """Recursively search the specified file path. May return either a Collection
+ or ArvadosFile.
+
+ :create:
+ If true, create path components (i.e. Collections) that are
+ missing. If "create" is False, return None if a path component is
+ not found.
+
+ :create_collection:
+ If the path is not found, "create" is True, and
+ "create_collection" is False, then create and return a new
+ ArvadosFile for the last path component. If "create_collection" is
+ True, then create and return a new Collection for the last path
+ component.
+
+ """
+ if create and self.sync_mode() == SYNC_READONLY:
+ raise IOError((errno.EROFS, "Collection is read only"))
+
p = path.split("/")
if p[0] == '.':
del p[0]
- if len(p) > 0:
+ if p and p[0]:
item = self._items.get(p[0])
if len(p) == 1:
# item must be a file
if item is None and create:
# create new file
if create_collection:
- item = Collection(parent=self, num_retries=self.num_retries)
+ item = Subcollection(self)
else:
item = ArvadosFile(self)
self._items[p[0]] = item
+ self.notify(self, ADD, p[0], item)
return item
else:
if item is None and create:
# create new collection
- item = Collection(parent=self, num_retries=self.num_retries)
+ item = Subcollection(self)
self._items[p[0]] = item
+ self.notify(self, ADD, p[0], item)
del p[0]
return item.find("/".join(p), create=create)
else:
return self
- @_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
-
def open(self, path, mode):
+ """Open a file-like object for access.
+
+ :path:
+ path to a file in the collection
+ :mode:
+ one of "r", "r+", "w", "w+", "a", "a+"
+ :"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.
+ """
mode = mode.replace("b", "")
if len(mode) == 0 or mode[0] not in ("r", "w", "a"):
raise ArgumentError("Bad mode '%s'" % mode)
create = (mode != "r")
+ if create and self.sync_mode() == SYNC_READONLY:
+ raise IOError((errno.EROFS, "Collection is read only"))
+
f = self.find(path, create=create)
+
if f is None:
raise IOError((errno.ENOENT, "File not found"))
if not isinstance(f, ArvadosFile):
f.truncate(0)
if mode == "r":
- return ArvadosFileReader(f, path, mode)
+ return ArvadosFileReader(f, path, mode, num_retries=self.num_retries)
else:
- return ArvadosFileWriter(f, path, mode)
+ return ArvadosFileWriter(f, path, mode, num_retries=self.num_retries)
- @_populate_first
+ @_synchronized
def modified(self):
+ """Test if the collection (or any subcollection or file) has been modified
+ since it was created."""
for k,v in self._items.items():
if v.modified():
return True
return False
- @_populate_first
+ @_synchronized
def set_unmodified(self):
+ """Recursively clear modified flag"""
for k,v in self._items.items():
v.set_unmodified()
- @_populate_first
+ @_synchronized
def __iter__(self):
- return self._items.iterkeys()
+ """Iterate over names of files and collections contained in this collection."""
+ return self._items.keys()
- @_populate_first
+ @_synchronized
def iterkeys(self):
- return self._items.iterkeys()
+ """Iterate over names of files and collections directly contained in this collection."""
+ return self._items.keys()
- @_populate_first
+ @_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]
- @_populate_first
+ @_synchronized
def __contains__(self, k):
+ """If there is a file or collection a directly contained by this collection
+ with name "k"."""
return k in self._items
- @_populate_first
+ @_synchronized
def __len__(self):
- return len(self._items)
+ """Get the number of items directly contained in this collection"""
+ return len(self._items)
- @_populate_first
+ @_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.notify(self, DEL, p, None)
- @_populate_first
+ @_synchronized
def keys(self):
+ """Get a list of names of files and collections directly contained in this collection."""
return self._items.keys()
- @_populate_first
+ @_synchronized
def values(self):
+ """Get a list of files and collection objects directly contained in this collection."""
return self._items.values()
- @_populate_first
+ @_synchronized
def items(self):
+ """Get a list of (name, object) tuples directly contained in this collection."""
return self._items.items()
- @_populate_first
def exists(self, path):
+ """Test if there is a file or collection at "path" """
return self.find(path) != None
- @_populate_first
- def remove(self, path):
+ @_must_be_writable
+ @_synchronized
+ def remove(self, path, rm_r=False):
+ """Remove the file or subcollection (directory) at `path`.
+ :rm_r:
+ Specify whether to remove non-empty subcollections (True), or raise an error (False).
+ """
p = path.split("/")
if p[0] == '.':
+ # Remove '.' from the front of the path
del p[0]
if len(p) > 0:
if item is None:
raise IOError((errno.ENOENT, "File not found"))
if len(p) == 1:
+ if isinstance(self._items[p[0]], SynchronizedCollectionBase) and len(self._items[p[0]]) > 0 and not rm_r:
+ raise IOError((errno.ENOTEMPTY, "Subcollection not empty"))
del self._items[p[0]]
+ self.notify(self, DEL, p[0], None)
else:
del p[0]
item.remove("/".join(p))
else:
raise IOError((errno.ENOENT, "File not found"))
- @_populate_first
+ def _cloneinto(self, target):
+ for k,v in self._items:
+ target._items[k] = v.clone(new_parent=target)
+
+ def clone(self):
+ raise NotImplementedError()
+
+ @_must_be_writable
+ @_synchronized
+ def copy(self, source_path, target_path, source_collection=None, overwrite=False):
+ """
+ copyto('/foo', '/bar') will overwrite 'foo' if it exists.
+ copyto('/foo/', '/bar') will place 'bar' in subcollection 'foo'
+ """
+ if source_collection is None:
+ source_collection = self
+
+ # Find the object to copy
+ sp = source_path.split("/")
+ source_obj = source_collection.find(source_path)
+ if source_obj is None:
+ raise IOError((errno.ENOENT, "File not found"))
+
+ # Find parent collection the target path
+ tp = target_path.split("/")
+ target_dir = self.find("/".join(tp[0:-1]), create=True, create_collection=True)
+
+ # Determine the name to use.
+ target_name = tp[-1] if tp[-1] else sp[-1]
+
+ if target_name in target_dir:
+ if isinstance(target_dir[target_name], SynchronizedCollectionBase):
+ target_dir = target_dir[target_name]
+ target_name = sp[-1]
+ elif not overwrite:
+ raise IOError((errno.EEXIST, "File already exists"))
+
+ # Actually make the copy.
+ dup = source_obj.clone(target_dir)
+ with target_dir.lock:
+ target_dir._items[target_name] = dup
+
+ self.notify(target_dir, ADD, target_name, dup)
+
+
+ @_synchronized
def manifest_text(self, strip=False, normalize=False):
+ """Get the manifest text for this collection, sub collections and files.
+
+ :strip:
+ If True, remove signing tokens from block locators if present.
+ If False, 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 and the collection
+ is not modified, return the original manifest text even if it is not
+ in normalized form.
+
+ """
if self.modified() or self._manifest_text is None or normalize:
return export_manifest(self, stream_name=".", portable_locators=strip)
else:
else:
return self._manifest_text
+ @_must_be_writable
+ @_synchronized
+ def merge(self, other):
+ for k in other.keys():
+ if k in self:
+ if isinstance(self[k], Subcollection) and isinstance(other[k], Subcollection):
+ self[k].merge(other[k])
+ else:
+ if self[k] != other[k]:
+ name = "%s~conflict-%s~" % (k, time.strftime("%Y-%m-%d_%H:%M%:%S",
+ time.gmtime()))
+ self[name] = other[k].clone(self)
+ self.notify(self, name, ADD, self[name])
+ else:
+ self[k] = other[k].clone(self)
+ self.notify(self, k, ADD, self[k])
+
def portable_data_hash(self):
+ """Get the portable data hash for this collection's manifest."""
stripped = self.manifest_text(strip=True)
return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
- @_populate_first
- def save(self, no_locator=False):
+
+class Collection(SynchronizedCollectionBase):
+ """Store an Arvados collection, consisting of a set of files and
+ sub-collections.
+ """
+
+ def __init__(self, manifest_locator_or_text=None,
+ parent=None,
+ config=None,
+ api_client=None,
+ keep_client=None,
+ num_retries=None,
+ block_manager=None,
+ sync=SYNC_READONLY):
+ """:manifest_locator_or_text:
+ One of Arvados collection UUID, block locator of
+ a manifest, raw manifest text, or None (to create an empty collection).
+ :parent:
+ the parent Collection, may be None.
+ :config:
+ the arvados configuration to get the hostname and 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 `config`.
+ :keep_client:
+ the Keep client to use for requests. If not specified, create one using `config`.
+ :num_retries:
+ the number of retries for API and Keep requests.
+ :block_manager:
+ the block manager to use. If not specified, create one.
+ :sync:
+ Set synchronization policy with API server collection record.
+ :SYNC_READONLY:
+ Collection is read only. No synchronization. This mode will
+ also forego locking, which gives better performance.
+ :SYNC_EXPLICIT:
+ Synchronize on explicit request via `update()` or `save()`
+ :SYNC_LIVE:
+ Synchronize with server in response to background websocket events,
+ on block write, or on file close.
+
+ """
+ super(Collection, self).__init__(parent)
+ self._api_client = api_client
+ self._keep_client = keep_client
+ self._block_manager = block_manager
+ self._config = config
+ self.num_retries = num_retries
+ self._manifest_locator = None
+ self._manifest_text = None
+ self._api_response = None
+ self._sync = sync
+ self.lock = threading.RLock()
+ self.callbacks = []
+ self.events = None
+
+ if manifest_locator_or_text:
+ if re.match(util.keep_locator_pattern, manifest_locator_or_text):
+ self._manifest_locator = manifest_locator_or_text
+ elif re.match(util.collection_uuid_pattern, manifest_locator_or_text):
+ self._manifest_locator = manifest_locator_or_text
+ elif re.match(util.manifest_pattern, manifest_locator_or_text):
+ self._manifest_text = manifest_locator_or_text
+ else:
+ raise errors.ArgumentError(
+ "Argument to CollectionReader must be a manifest or a collection UUID")
+
+ self._populate()
+
+ if self._sync == SYNC_LIVE:
+ if not self._manifest_locator or not re.match(util.collection_uuid_pattern, self._manifest_locator):
+ raise errors.ArgumentError("Cannot SYNC_LIVE unless a collection uuid is specified")
+ self.events = events.subscribe(arvados.api(), [["object_uuid", "=", self._manifest_locator]], self.on_message)
+
+ @staticmethod
+ def create(name, owner_uuid=None, sync=SYNC_EXPLICIT):
+ c = Collection(sync=sync)
+ c.save_as(name, owner_uuid=owner_uuid, ensure_unique_name=True)
+ return c
+
+ def _root_lock(self):
+ return self.lock
+
+ def sync_mode(self):
+ return self._sync
+
+ def on_message(self):
+ self.update()
+
+ @_synchronized
+ def update(self):
+ n = self._my_api().collections().get(uuid=self._manifest_locator, select=["manifest_text"]).execute()
+ other = import_collection(n["manifest_text"])
+ self.merge(other)
+
+ @_synchronized
+ def _my_api(self):
+ if self._api_client is None:
+ self._api_client = arvados.SafeApi(self._config)
+ 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=self._api_client)
+ return self._keep_client
+
+ @_synchronized
+ def _my_block_manager(self):
+ if self._block_manager is None:
+ self._block_manager = BlockManager(self._my_keep())
+ return self._block_manager
+
+ def _populate_from_api_server(self):
+ # As in KeepClient itself, we must wait until the last
+ # possible moment to instantiate an API client, in order to
+ # avoid tripping up clients that don't have access to an API
+ # server. If we do build one, make sure our Keep client uses
+ # it. If instantiation fails, we'll fall back to the except
+ # clause, just like any other Collection lookup
+ # failure. Return an exception, or None if successful.
+ try:
+ self._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']
+ return None
+ except Exception as e:
+ return e
+
+ def _populate_from_keep(self):
+ # Retrieve a manifest directly from Keep. This has a chance of
+ # working if [a] the locator includes a permission signature
+ # or [b] the Keep services are operating in world-readable
+ # mode. Return an exception, or None if successful.
+ try:
+ self._manifest_text = self._my_keep().get(
+ self._manifest_locator, num_retries=self.num_retries)
+ except Exception as e:
+ return e
+
+ def _populate(self):
+ if self._manifest_locator is None and self._manifest_text is None:
+ return
+ error_via_api = None
+ error_via_keep = None
+ should_try_keep = ((self._manifest_text is None) and
+ util.keep_locator_pattern.match(
+ self._manifest_locator))
+ if ((self._manifest_text is None) and
+ util.signed_locator_pattern.match(self._manifest_locator)):
+ error_via_keep = self._populate_from_keep()
+ if self._manifest_text is None:
+ error_via_api = self._populate_from_api_server()
+ if error_via_api is not None and not should_try_keep:
+ raise error_via_api
+ if ((self._manifest_text is None) and
+ not error_via_keep and
+ should_try_keep):
+ # Looks like a keep locator, and we didn't already try keep above
+ error_via_keep = self._populate_from_keep()
+ if self._manifest_text is None:
+ # Nothing worked!
+ raise arvados.errors.NotFoundError(
+ ("Failed to retrieve collection '{}' " +
+ "from either API server ({}) or Keep ({})."
+ ).format(
+ self._manifest_locator,
+ error_via_api,
+ error_via_keep))
+ # populate
+ import_manifest(self._manifest_text, self)
+
+ if self._sync == SYNC_READONLY:
+ # Now that we're populated, knowing that this will be readonly,
+ # forego any further locking.
+ self.lock = NoopLock()
+
+ def __enter__(self):
+ return self
+
+ def __exit__(self, exc_type, exc_value, traceback):
+ """Support scoped auto-commit in a with: block"""
+ if self._sync != SYNC_READONLY:
+ self.save(allow_no_locator=True)
+ if self._block_manager is not None:
+ self._block_manager.stop_threads()
+
+ @_synchronized
+ def clone(self, new_parent=None, new_sync=SYNC_READONLY, new_config=None):
+ if new_config is None:
+ new_config = self.config
+ c = Collection(parent=new_parent, config=new_config, sync=new_sync)
+ if new_sync == SYNC_READONLY:
+ c.lock = NoopLock()
+ c._items = {}
+ self._cloneinto(c)
+ return c
+
+ @_synchronized
+ 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
+
+ @_must_be_writable
+ @_synchronized
+ def save(self, allow_no_locator=False):
+ """Commit pending buffer blocks to Keep, write the manifest to Keep, and
+ update the collection record to Keep.
+
+ :allow_no_locator:
+ If there is no collection uuid associated with this
+ Collection and `allow_no_locator` is False, raise an error. If True,
+ do not raise an error.
+ """
if self.modified():
self._my_block_manager().commit_all()
self._my_keep().put(self.manifest_text(strip=True))
body={'manifest_text': self.manifest_text(strip=False)}
).execute(
num_retries=self.num_retries)
- elif not no_locator:
+ elif not allow_no_locator:
raise AssertionError("Collection manifest_locator must be a collection uuid. Use save_as() for new collections.")
self.set_unmodified()
- @_populate_first
+ @_must_be_writable
+ @_synchronized
def save_as(self, name, owner_uuid=None, ensure_unique_name=False):
+ """Save a new collection record.
+
+ :name:
+ The collection name.
+
+ :owner_uuid:
+ the user, or project uuid that will own this collection.
+ If None, defaults to the current user.
+
+ :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.
+
+ """
self._my_block_manager().commit_all()
self._my_keep().put(self.manifest_text(strip=True))
body = {"manifest_text": self.manifest_text(strip=False),
if owner_uuid:
body["owner_uuid"] = owner_uuid
self._api_response = self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=self.num_retries)
+
+ if self.events:
+ self.events.unsubscribe(filters=[["object_uuid", "=", self._manifest_locator]])
+
self._manifest_locator = self._api_response["uuid"]
+
+ if self.events:
+ self.events.subscribe(filters=[["object_uuid", "=", self._manifest_locator]])
+
self.set_unmodified()
- @_populate_first
- def rename(self, old, new):
- old_path, old_fn = os.path.split(old)
- old_col = self.find(path)
- if old_col is None:
- raise IOError((errno.ENOENT, "File not found"))
- if not isinstance(old_p, Collection):
- raise IOError((errno.ENOTDIR, "Parent in path is a file, not a directory"))
- if old_fn in old_col:
- new_path, new_fn = os.path.split(new)
- new_col = self.find(new_path, create=True, create_collection=True)
- if not isinstance(new_col, Collection):
- raise IOError((errno.ENOTDIR, "Destination is a file, not a directory"))
- ent = old_col[old_fn]
- del old_col[old_fn]
- ent.parent = new_col
- new_col[new_fn] = ent
- else:
- raise IOError((errno.ENOENT, "File not found"))
+ @_synchronized
+ def subscribe(self, callback):
+ self.callbacks.append(callback)
+
+ @_synchronized
+ def unsubscribe(self, callback):
+ self.callbacks.remove(callback)
+
+ @_synchronized
+ def notify(self, collection, event, name, item):
+ for c in self.callbacks:
+ c(collection, event, name, item)
+
+class Subcollection(SynchronizedCollectionBase):
+ """This is a subdirectory within a collection that doesn't have its own API
+ server record. It falls under the umbrella of the root collection."""
+
+ def __init__(self, parent):
+ super(Subcollection, self).__init__(parent)
+ self.lock = parent._root_lock()
-def import_manifest(manifest_text, into_collection=None, api_client=None, keep=None, num_retries=None):
+ def _root_lock(self):
+ return self.parent._root_lock()
+
+ def sync_mode(self):
+ return self.parent.sync_mode()
+
+ def _my_api(self):
+ return self.parent._my_api()
+
+ def _my_keep(self):
+ return self.parent._my_keep()
+
+ def _my_block_manager(self):
+ return self.parent._my_block_manager()
+
+ def _populate(self):
+ self.parent._populate()
+
+ def notify(self, collection, event, name, item):
+ self.parent.notify(collection, event, name, item)
+
+ @_synchronized
+ def clone(self, new_parent):
+ c = Subcollection(new_parent)
+ c._items = {}
+ self._cloneinto(c)
+ return c
+
+def import_manifest(manifest_text,
+ into_collection=None,
+ api_client=None,
+ keep=None,
+ num_retries=None,
+ sync=SYNC_READONLY):
+ """Import a manifest into a `Collection`.
+
+ :manifest_text:
+ The manifest text to import from.
+
+ :into_collection:
+ The `Collection` that will be initialized (must be empty).
+ If None, create a new `Collection` object.
+
+ :api_client:
+ The API client object that will be used when creating a new `Collection` object.
+
+ :keep:
+ The keep client object that will be used when creating a new `Collection` object.
+
+ :num_retries:
+ the default number of api client and keep retries on error.
+
+ :sync:
+ Collection sync mode (only if into_collection is None)
+ """
if into_collection is not None:
if len(into_collection) > 0:
raise ArgumentError("Can only import manifest into an empty collection")
c = into_collection
else:
- c = Collection(api_client=api_client, keep_client=keep, num_retries=num_retries)
+ c = Collection(api_client=api_client, keep_client=keep, num_retries=num_retries, sync=sync)
+
+ save_sync = c.sync_mode()
+ c._sync = None
STREAM_NAME = 0
BLOCKS = 1
state = STREAM_NAME
c.set_unmodified()
+ c._sync = save_sync
return c
def export_manifest(item, stream_name=".", portable_locators=False):
+ """
+ :item:
+ Create a manifest for `item` (must be a `Collection` or `ArvadosFile`). If
+ `item` is a is a `Collection`, this will also export subcollections.
+
+ :stream_name:
+ the name of the stream when exporting `item`.
+
+ :portable_locators:
+ If True, strip any permission hints on block locators.
+ If False, use block locators as-is.
+ """
buf = ""
- if isinstance(item, Collection):
+ if isinstance(item, SynchronizedCollectionBase):
stream = {}
sorted_keys = sorted(item.keys())
for k in [s for s in sorted_keys if isinstance(item[s], ArvadosFile)]:
v = item[k]
st = []
- for s in v.segments:
+ for s in v.segments():
loc = s.locator
if loc.startswith("bufferblock"):
loc = v.parent._my_block_manager()._bufferblocks[loc].locator()
if stream:
buf += ' '.join(normalize_stream(stream_name, stream))
buf += "\n"
- for k in [s for s in sorted_keys if isinstance(item[s], Collection)]:
+ for k in [s for s in sorted_keys if isinstance(item[s], SynchronizedCollectionBase)]:
buf += export_manifest(item[k], stream_name=os.path.join(stream_name, k), portable_locators=portable_locators)
elif isinstance(item, ArvadosFile):
st = []
projects / arvados.git / blobdiff