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')
for sline in self._manifest_text.split("\n")
if sline]
- @staticmethod
def _populate_first(orig_func):
# Decorator for methods that read actual Collection data.
@functools.wraps(orig_func)
"resumable writer can't accept unsourced data")
return super(ResumableCollectionWriter, self).write(data)
+ADD = "add"
+DEL = "del"
class SynchronizedCollectionBase(CollectionBase):
- SYNC_READONLY = 1
- SYNC_EXPLICIT = 2
- SYNC_LIVE = 3
-
def __init__(self, parent=None):
self.parent = parent
- self._items = None
+ self._items = {}
def _my_api(self):
raise NotImplementedError()
def _populate(self):
raise NotImplementedError()
- def _sync_mode(self):
+ def sync_mode(self):
raise NotImplementedError()
- @staticmethod
- 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
+ def notify(self, collection, event, name, item):
+ raise NotImplementedError()
- @arvfile._synchronized
- @_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.
component.
"""
- if create and self._sync_mode() == SynchronizedCollectionBase.SYNC_READONLY:
+ 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
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 = 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:
raise ArgumentError("Bad mode '%s'" % mode)
create = (mode != "r")
- if create and self._sync_mode() == SynchronizedCollectionBase.SYNC_READONLY:
+ 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)
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def modified(self):
"""Test if the collection (or any subcollection or file) has been modified
since it was created."""
return True
return False
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def set_unmodified(self):
"""Recursively clear modified flag"""
for k,v in self._items.items():
v.set_unmodified()
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def __iter__(self):
"""Iterate over names of files and collections contained in this collection."""
return self._items.keys()
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def iterkeys(self):
"""Iterate over names of files and collections directly contained in this collection."""
return self._items.keys()
- @arvfile._synchronized
- @_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]
- @arvfile._synchronized
- @_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
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def __len__(self):
"""Get the number of items directly contained in this collection"""
return len(self._items)
@_must_be_writable
- @arvfile._synchronized
- @_populate_first
+ @_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)
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def keys(self):
"""Get a list of names of files and collections directly contained in this collection."""
return self._items.keys()
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def values(self):
"""Get a list of files and collection objects directly contained in this collection."""
return self._items.values()
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def items(self):
"""Get a list of (name, object) tuples directly contained in this collection."""
return self._items.items()
return self.find(path) != None
@_must_be_writable
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def remove(self, path, rm_r=False):
"""Remove the file or subcollection (directory) at `path`.
:rm_r:
if item is None:
raise IOError((errno.ENOENT, "File not found"))
if len(p) == 1:
- if isinstance(SynchronizedCollection, self._items[p[0]]) and len(self._items[p[0]]) > 0 and not rm_r:
+ 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))
raise IOError((errno.ENOENT, "File not found"))
def _cloneinto(self, target):
- for k,v in self._items:
- target._items[k] = v.clone(new_parent=target)
+ for k,v in self._items.items():
+ target._items[k] = v.clone(target)
def clone(self):
raise NotImplementedError()
- @arvfile._synchronized
- @_populate_first
+ @_must_be_writable
+ @_synchronized
+ def copy(self, source_path, target_path, source_collection=None, overwrite=False):
+ """Copy a file or subcollection to a new path in this collection.
+
+ :source_path:
+ 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.
+ """
+ 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.
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._items[name] = other[k].clone(self)
+ self.notify(self, name, ADD, self[name])
+ else:
+ self._items[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)
config=None,
api_client=None,
keep_client=None,
- num_retries=0,
+ num_retries=None,
block_manager=None,
- sync=Collection.SYNC_READONLY):
+ 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).
Collection is read only. No synchronization. This mode will
also forego locking, which gives better performance.
:SYNC_EXPLICIT:
- Synchronize on explicit request via `merge()` or `save()`
+ 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.
"""
-
- self.parent = parent
- self._items = None
+ super(Collection, self).__init__(parent)
self._api_client = api_client
self._keep_client = keep_client
self._block_manager = block_manager
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):
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
- @arvfile._synchronized
+ 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.api.SafeApi(self._config)
+ self._api_client = arvados.SafeApi(self._config)
self._keep_client = self._api_client.keep
return self._api_client
- @arvfile._synchronized
+ @_synchronized
def _my_keep(self):
if self._keep_client is None:
if self._api_client is None:
self._keep_client = KeepClient(api=self._api_client)
return self._keep_client
- @arvfile._synchronized
+ @_synchronized
def _my_block_manager(self):
if self._block_manager is None:
self._block_manager = BlockManager(self._my_keep())
return e
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))
+ 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()
def __exit__(self, exc_type, exc_value, traceback):
"""Support scoped auto-commit in a with: block"""
- self.save(allow_no_locator=True)
+ if self._sync != SYNC_READONLY:
+ self.save(allow_no_locator=True)
if self._block_manager is not None:
self._block_manager.stop_threads()
- @arvfile._synchronized
- @_populate_first
- def clone(self, new_parent=None, new_sync=Collection.SYNC_READONLY, new_config=self.config):
+ @_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 == Collection.SYNC_READONLY:
+ if new_sync == SYNC_READONLY:
c.lock = NoopLock()
c._items = {}
self._cloneinto(c)
return c
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def api_response(self):
"""
api_response() -> dict or None
return self._api_response
@_must_be_writable
- @arvfile._synchronized
- @_populate_first
+ @_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.
self.set_unmodified()
@_must_be_writable
- @arvfile._synchronized
- @_populate_first
+ @_synchronized
def save_as(self, name, owner_uuid=None, ensure_unique_name=False):
"""Save a new collection record.
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()
+ @_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
super(Subcollection, self).__init__(parent)
self.lock = parent._root_lock()
- def _root_lock():
+ def _root_lock(self):
return self.parent._root_lock()
def sync_mode(self):
def _populate(self):
self.parent._populate()
- @arvfile._synchronized
- @_populate_first
+ def notify(self, collection, event, name, item):
+ self.parent.notify(collection, event, name, item)
+
+ @_synchronized
def clone(self, new_parent):
- c = Subcollection(parent=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):
+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:
:keep:
The keep client object that will be used when creating a new `Collection` object.
- num_retries
+ :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):
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()
projects / arvados.git / blobdiff