14880: Fix help message typo.

[arvados.git] / sdk / python / arvados / collection.py

diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py
index 1047f5382dd50c84bc496c85d915222715e83e29..cf1a36f9fdfbbfdf739fe75027d00eaa782df4f2 100644 (file)
--- a/sdk/python/arvados/collection.py
+++ b/sdk/python/arvados/collection.py
@@ -1,30 +1,60 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+from __future__ import absolute_import
+from future.utils import listitems, listvalues, viewkeys
+from builtins import str
+from past.builtins import basestring
+from builtins import object
+import ciso8601
+import datetime
+import errno

 import functools
 import functools

+import hashlib
+import io

 import logging
 import os
 import re
 import logging
 import os
 import re

-import errno
-import hashlib
-import time
+import sys

 import threading
 import threading

+import time

 
 from collections import deque
 from stat import *
 
 
 from collections import deque
 from stat import *
 

-from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, _BlockManager, synchronized, must_be_writable, NoopLock
-from keep import KeepLocator, KeepClient
+from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, WrappableFile, _BlockManager, synchronized, must_be_writable, NoopLock
+from .keep import KeepLocator, KeepClient

 from .stream import StreamReader
 from .stream import StreamReader

-from ._normalize_stream import normalize_stream
+from ._normalize_stream import normalize_stream, escape

 from ._ranges import Range, LocatorAndRange
 from .safeapi import ThreadSafeApiCache
 from ._ranges import Range, LocatorAndRange
 from .safeapi import ThreadSafeApiCache

-import config
-import errors
-import util
-import events
+import arvados.config as config
+import arvados.errors as errors
+import arvados.util
+import arvados.events as events

 from arvados.retry import retry_method
 
 _logger = logging.getLogger('arvados.collection')
 
 from arvados.retry import retry_method
 
 _logger = logging.getLogger('arvados.collection')
 

+
+if sys.version_info >= (3, 0):
+    TextIOWrapper = io.TextIOWrapper
+else:
+    class TextIOWrapper(io.TextIOWrapper):
+        """To maintain backward compatibility, cast str to unicode in
+        write('foo').
+
+        """
+        def write(self, data):
+            if isinstance(data, basestring):
+                data = unicode(data)
+            return super(TextIOWrapper, self).write(data)
+
+

 class CollectionBase(object):
 class CollectionBase(object):

+    """Abstract base class for Collection classes."""
+

     def __enter__(self):
         return self
 
     def __enter__(self):
         return self
 


@@ -51,7 +81,7 @@ class CollectionBase(object):
             if fields:
                 clean_fields = fields[:1] + [
                     (re.sub(r'\+[^\d][^\+]*', '', x)
             if fields:
                 clean_fields = fields[:1] + [
                     (re.sub(r'\+[^\d][^\+]*', '', x)

-                     if re.match(util.keep_locator_pattern, x)
+                     if re.match(arvados.util.keep_locator_pattern, x)

                      else x)
                     for x in fields[1:]]
                 clean += [' '.join(clean_fields), "\n"]
                      else x)
                     for x in fields[1:]]
                 clean += [' '.join(clean_fields), "\n"]


@@ -82,6 +112,8 @@ class _WriterFile(_FileLikeObjectBase):
 
 
 class CollectionWriter(CollectionBase):
 
 
 class CollectionWriter(CollectionBase):

+    """Deprecated, use Collection instead."""
+

     def __init__(self, api_client=None, num_retries=0, replication=None):
         """Instantiate a CollectionWriter.
 
     def __init__(self, api_client=None, num_retries=0, replication=None):
         """Instantiate a CollectionWriter.
 


@@ -180,7 +212,7 @@ class CollectionWriter(CollectionBase):
 
     def _work_trees(self):
         path, stream_name, max_manifest_depth = self._queued_trees[0]
 
     def _work_trees(self):
         path, stream_name, max_manifest_depth = self._queued_trees[0]

-        d = util.listdir_recursive(
+        d = arvados.util.listdir_recursive(

             path, max_depth = (None if max_manifest_depth == 0 else 0))
         if d:
             self._queue_dirents(stream_name, d)
             path, max_depth = (None if max_manifest_depth == 0 else 0))
         if d:
             self._queue_dirents(stream_name, d)


@@ -216,7 +248,11 @@ class CollectionWriter(CollectionBase):
         self.do_queued_work()
 
     def write(self, newdata):
         self.do_queued_work()
 
     def write(self, newdata):

-        if hasattr(newdata, '__iter__'):
+        if isinstance(newdata, bytes):
+            pass
+        elif isinstance(newdata, str):
+            newdata = newdata.encode()
+        elif hasattr(newdata, '__iter__'):

             for s in newdata:
                 self.write(s)
             return
             for s in newdata:
                 self.write(s)
             return


@@ -247,7 +283,7 @@ class CollectionWriter(CollectionBase):
             streampath, filename = split(streampath)
         if self._last_open and not self._last_open.closed:
             raise errors.AssertionError(
             streampath, filename = split(streampath)
         if self._last_open and not self._last_open.closed:
             raise errors.AssertionError(

-                "can't open '{}' when '{}' is still open".format(
+                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)
                     filename, self._last_open.name))
         if streampath != self.current_stream_name():
             self.start_new_stream(streampath)


@@ -256,7 +292,7 @@ class CollectionWriter(CollectionBase):
         return self._last_open
 
     def flush_data(self):
         return self._last_open
 
     def flush_data(self):

-        data_buffer = ''.join(self._data_buffer)
+        data_buffer = b''.join(self._data_buffer)

         if data_buffer:
             self._current_stream_locators.append(
                 self._my_keep().put(
         if data_buffer:
             self._current_stream_locators.append(
                 self._my_keep().put(


@@ -307,7 +343,8 @@ class CollectionWriter(CollectionBase):
     def set_current_stream_name(self, newstreamname):
         if re.search(r'[\t\n]', newstreamname):
             raise errors.AssertionError(
     def set_current_stream_name(self, newstreamname):
         if re.search(r'[\t\n]', newstreamname):
             raise errors.AssertionError(

-                "Manifest stream names cannot contain whitespace")
+                "Manifest stream names cannot contain whitespace: '%s'" %
+                (newstreamname))

         self._current_stream_name = '.' if newstreamname=='' else newstreamname
 
     def current_stream_name(self):
         self._current_stream_name = '.' if newstreamname=='' else newstreamname
 
     def current_stream_name(self):


@@ -345,11 +382,12 @@ class CollectionWriter(CollectionBase):
         sending manifest_text() to the API server's "create
         collection" endpoint.
         """
         sending manifest_text() to the API server's "create
         collection" endpoint.
         """

-        return self._my_keep().put(self.manifest_text(), copies=self.replication)
+        return self._my_keep().put(self.manifest_text().encode(),
+                                   copies=self.replication)

 
     def portable_data_hash(self):
 
     def portable_data_hash(self):

-        stripped = self.stripped_manifest()
-        return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
+        stripped = self.stripped_manifest().encode()
+        return '{}+{}'.format(hashlib.md5(stripped).hexdigest(), len(stripped))

 
     def manifest_text(self):
         self.finish_current_stream()
 
     def manifest_text(self):
         self.finish_current_stream()


@@ -371,8 +409,18 @@ class CollectionWriter(CollectionBase):
             ret += locators
         return ret
 
             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)
+

 
 class ResumableCollectionWriter(CollectionWriter):
 
 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',
     STATE_PROPS = ['_current_stream_files', '_current_stream_length',
                    '_current_stream_locators', '_current_stream_name',
                    '_current_file_name', '_current_file_pos', '_close_file',


@@ -413,22 +461,22 @@ class ResumableCollectionWriter(CollectionWriter):
                 writer._queued_file.seek(pos)
             except IOError as error:
                 raise errors.StaleWriterStateError(
                 writer._queued_file.seek(pos)
             except IOError as error:
                 raise errors.StaleWriterStateError(

-                    "failed to reopen active file {}: {}".format(path, error))
+                    u"failed to reopen active file {}: {}".format(path, error))

         return writer
 
     def check_dependencies(self):
         return writer
 
     def check_dependencies(self):

-        for path, orig_stat in self._dependencies.items():
+        for path, orig_stat in listitems(self._dependencies):

             if not S_ISREG(orig_stat[ST_MODE]):
             if not S_ISREG(orig_stat[ST_MODE]):

-                raise errors.StaleWriterStateError("{} not file".format(path))
+                raise errors.StaleWriterStateError(u"{} not file".format(path))

             try:
                 now_stat = tuple(os.stat(path))
             except OSError as error:
                 raise errors.StaleWriterStateError(
             try:
                 now_stat = tuple(os.stat(path))
             except OSError as error:
                 raise errors.StaleWriterStateError(

-                    "failed to stat {}: {}".format(path, error))
+                    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])):
             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("{} changed".format(path))
+                raise errors.StaleWriterStateError(u"{} changed".format(path))

 
     def dump_state(self, copy_func=lambda x: x):
         state = {attr: copy_func(getattr(self, attr))
 
     def dump_state(self, copy_func=lambda x: x):
         state = {attr: copy_func(getattr(self, attr))


@@ -444,7 +492,7 @@ class ResumableCollectionWriter(CollectionWriter):
         try:
             src_path = os.path.realpath(source)
         except Exception:
         try:
             src_path = os.path.realpath(source)
         except Exception:

-            raise errors.AssertionError("{} not a file path".format(source))
+            raise errors.AssertionError(u"{} not a file path".format(source))

         try:
             path_stat = os.stat(src_path)
         except OSError as stat_error:
         try:
             path_stat = os.stat(src_path)
         except OSError as stat_error:


@@ -457,10 +505,10 @@ class ResumableCollectionWriter(CollectionWriter):
             self._dependencies[source] = tuple(fd_stat)
         elif path_stat is None:
             raise errors.AssertionError(
             self._dependencies[source] = tuple(fd_stat)
         elif path_stat is None:
             raise errors.AssertionError(

-                "could not stat {}: {}".format(source, stat_error))
+                u"could not stat {}: {}".format(source, stat_error))

         elif path_stat.st_ino != fd_stat.st_ino:
             raise errors.AssertionError(
         elif path_stat.st_ino != fd_stat.st_ino:
             raise errors.AssertionError(

-                "{} changed between open and stat calls".format(source))
+                u"{} changed between open and stat calls".format(source))

         else:
             self._dependencies[src_path] = tuple(fd_stat)
 
         else:
             self._dependencies[src_path] = tuple(fd_stat)
 


@@ -489,6 +537,7 @@ class RichCollectionBase(CollectionBase):
     def __init__(self, parent=None):
         self.parent = parent
         self._committed = False
     def __init__(self, parent=None):
         self.parent = parent
         self._committed = False

+        self._has_remote_blocks = False

         self._callback = None
         self._items = {}
 
         self._callback = None
         self._items = {}
 


@@ -513,6 +562,24 @@ class RichCollectionBase(CollectionBase):
     def stream_name(self):
         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):
     @must_be_writable
     @synchronized
     def find_or_create(self, path, create_type):


@@ -543,7 +610,7 @@ class RichCollectionBase(CollectionBase):
                     else:
                         item = ArvadosFile(self, pathcomponents[0])
                     self._items[pathcomponents[0]] = item
                     else:
                         item = ArvadosFile(self, pathcomponents[0])
                     self._items[pathcomponents[0]] = item

-                    self._committed = False
+                    self.set_committed(False)

                     self.notify(ADD, self, pathcomponents[0], item)
                 return item
             else:
                     self.notify(ADD, self, pathcomponents[0], item)
                 return item
             else:


@@ -551,12 +618,12 @@ class RichCollectionBase(CollectionBase):
                     # create new collection
                     item = Subcollection(self, pathcomponents[0])
                     self._items[pathcomponents[0]] = item
                     # create new collection
                     item = Subcollection(self, pathcomponents[0])
                     self._items[pathcomponents[0]] = item

-                    self._committed = False
+                    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:
                     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: '%s'" % pathcomponents[0])
+                    raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0])

         else:
             return self
 
         else:
             return self
 


@@ -564,16 +631,23 @@ class RichCollectionBase(CollectionBase):
     def find(self, path):
         """Recursively search the specified file path.
 
     def find(self, path):
         """Recursively search the specified file path.
 

-        May return either a Collection or ArvadosFile.  Return None if not
+        May return either a Collection or ArvadosFile. Return None if not

         found.
         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 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])
         item = self._items.get(pathcomponents[0])

-        if len(pathcomponents) == 1:
+        if item is None:
+            return None
+        elif len(pathcomponents) == 1:

             return item
         else:
             if isinstance(item, RichCollectionBase):
             return item
         else:
             if isinstance(item, RichCollectionBase):


@@ -582,7 +656,7 @@ class RichCollectionBase(CollectionBase):
                 else:
                     return item
             else:
                 else:
                     return item
             else:

-                raise IOError(errno.ENOTDIR, "Is not a directory: %s" % pathcomponents[0])
+                raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0])

 
     @synchronized
     def mkdirs(self, path):
 
     @synchronized
     def mkdirs(self, path):


@@ -594,17 +668,22 @@ class RichCollectionBase(CollectionBase):
         """
 
         if self.find(path) != None:
         """
 
         if self.find(path) != None:

-            raise IOError(errno.EEXIST, "Directory or file exists: '%s'" % path)
+            raise IOError(errno.EEXIST, "Directory or file exists", path)

 
         return self.find_or_create(path, COLLECTION)
 
 
         return self.find_or_create(path, COLLECTION)
 

-    def open(self, path, mode="r"):
+    def open(self, path, mode="r", encoding=None):

         """Open a file-like object for access.
 
         :path:
           path to a file in the collection
         :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+"
+          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+":
           :"r":
             opens for reading
           :"r+":


@@ -615,34 +694,35 @@ class RichCollectionBase(CollectionBase):
             opens for reading and writing.  All writes are appended to
             the end of the file.  Writing does not affect the file pointer for
             reading.
             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 errors.ArgumentError("Bad mode '%s'" % mode)
-        create = (mode != "r")

 
 

-        if create and not self.writable():
-            raise IOError(errno.EROFS, "Collection is read only")
+        if not re.search(r'^[rwa][bt]?\+?$', mode):
+            raise errors.ArgumentError("Invalid mode {!r}".format(mode))

 
 

-        if create:
-            arvfile = self.find_or_create(path, FILE)
-        else:
+        if mode[0] == 'r' and '+' not in mode:
+            fclass = ArvadosFileReader

             arvfile = self.find(path)
             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:
 
         if arvfile is None:

-            raise IOError(errno.ENOENT, "File not found")
+            raise IOError(errno.ENOENT, "File not found", path)

         if not isinstance(arvfile, ArvadosFile):
         if not isinstance(arvfile, ArvadosFile):

-            raise IOError(errno.EISDIR, "Is a directory: %s" % path)
+            raise IOError(errno.EISDIR, "Is a directory", path)

 
 

-        if mode[0] == "w":
+        if mode[0] == 'w':

             arvfile.truncate(0)
 
             arvfile.truncate(0)
 

-        name = os.path.basename(path)
-
-        if mode == "r":
-            return ArvadosFileReader(arvfile, num_retries=self.num_retries)
-        else:
-            return ArvadosFileWriter(arvfile, mode, num_retries=self.num_retries)
+        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."""
 
     def modified(self):
         """Determine if the collection has been modified since last commited."""


@@ -651,25 +731,31 @@ class RichCollectionBase(CollectionBase):
     @synchronized
     def committed(self):
         """Determine if the collection has been committed to the API server."""
     @synchronized
     def committed(self):
         """Determine if the collection has been committed to the API server."""

-
-        if self._committed is False:
-            return False
-        for v in self._items.values():
-            if v.committed() is False:
-                return False
-        return True
+        return self._committed

 
     @synchronized
 
     @synchronized

-    def set_committed(self):
-        """Recursively set committed flag to True."""
-        self._committed = True
-        for k,v in self._items.items():
-            v.set_committed()
+    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."""
 
     @synchronized
     def __iter__(self):
         """Iterate over names of files and collections contained in this collection."""

-        return iter(self._items.keys())
+        return iter(viewkeys(self._items))

 
     @synchronized
     def __getitem__(self, k):
 
     @synchronized
     def __getitem__(self, k):


@@ -695,7 +781,7 @@ class RichCollectionBase(CollectionBase):
     def __delitem__(self, p):
         """Delete an item by name which is directly contained by this collection."""
         del self._items[p]
     def __delitem__(self, p):
         """Delete an item by name which is directly contained by this collection."""
         del self._items[p]

-        self._committed = False
+        self.set_committed(False)

         self.notify(DEL, self, p, None)
 
     @synchronized
         self.notify(DEL, self, p, None)
 
     @synchronized


@@ -706,12 +792,12 @@ class RichCollectionBase(CollectionBase):
     @synchronized
     def values(self):
         """Get a list of files and collection objects directly contained in this collection."""
     @synchronized
     def values(self):
         """Get a list of files and collection objects directly contained in this collection."""

-        return self._items.values()
+        return listvalues(self._items)

 
     @synchronized
     def items(self):
         """Get a list of (name, object) tuples directly contained in this collection."""
 
     @synchronized
     def items(self):
         """Get a list of (name, object) tuples directly contained in this collection."""

-        return self._items.items()
+        return listitems(self._items)

 
     def exists(self, path):
         """Test if there is a file or collection at `path`."""
 
     def exists(self, path):
         """Test if there is a file or collection at `path`."""


@@ -732,19 +818,19 @@ class RichCollectionBase(CollectionBase):
         pathcomponents = path.split("/", 1)
         item = self._items.get(pathcomponents[0])
         if item is None:
         pathcomponents = path.split("/", 1)
         item = self._items.get(pathcomponents[0])
         if item is None:

-            raise IOError(errno.ENOENT, "File not found")
+            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:
         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, "Subcollection not empty")
+                raise IOError(errno.ENOTEMPTY, "Directory not empty", path)

             deleteditem = self._items[pathcomponents[0]]
             del self._items[pathcomponents[0]]
             deleteditem = self._items[pathcomponents[0]]
             del self._items[pathcomponents[0]]

-            self._committed = False
+            self.set_committed(False)

             self.notify(DEL, self, pathcomponents[0], deleteditem)
         else:
             item.remove(pathcomponents[1])
 
     def _clonefrom(self, source):
             self.notify(DEL, self, pathcomponents[0], deleteditem)
         else:
             item.remove(pathcomponents[1])
 
     def _clonefrom(self, source):

-        for k,v in source.items():
+        for k,v in listitems(source):

             self._items[k] = v.clone(self, k)
 
     def clone(self):
             self._items[k] = v.clone(self, k)
 
     def clone(self):


@@ -773,7 +859,7 @@ class RichCollectionBase(CollectionBase):
         """
 
         if target_name in self and not overwrite:
         """
 
         if target_name in self and not overwrite:

-            raise IOError(errno.EEXIST, "File already exists")
+            raise IOError(errno.EEXIST, "File already exists", target_name)

 
         modified_from = None
         if target_name in self:
 
         modified_from = None
         if target_name in self:


@@ -787,7 +873,9 @@ class RichCollectionBase(CollectionBase):
             item = source_obj.clone(self, target_name)
 
         self._items[target_name] = item
             item = source_obj.clone(self, target_name)
 
         self._items[target_name] = item

-        self._committed = False
+        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))
 
         if modified_from:
             self.notify(MOD, self, target_name, (modified_from, item))


@@ -802,7 +890,7 @@ class RichCollectionBase(CollectionBase):
         if isinstance(source, basestring):
             source_obj = source_collection.find(source)
             if source_obj is None:
         if isinstance(source, basestring):
             source_obj = source_collection.find(source)
             if source_obj is None:

-                raise IOError(errno.ENOENT, "File not found")
+                raise IOError(errno.ENOENT, "File not found", source)

             sourcecomponents = source.split("/")
         else:
             source_obj = source
             sourcecomponents = source.split("/")
         else:
             source_obj = source


@@ -826,9 +914,9 @@ class RichCollectionBase(CollectionBase):
                 target_dir = self
 
         if target_dir is None:
                 target_dir = self
 
         if target_dir is None:

-            raise IOError(errno.ENOENT, "Target directory not found.")
+            raise IOError(errno.ENOENT, "Target directory not found", target_name)

 
 

-        if target_name in target_dir and isinstance(self[target_name], RichCollectionBase) and sourcecomponents:
+        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]
 
             target_dir = target_dir[target_name]
             target_name = sourcecomponents[-1]
 


@@ -881,7 +969,7 @@ class RichCollectionBase(CollectionBase):
 
         source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, False)
         if not source_obj.writable():
 
         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.")
+            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="."):
         target_dir.add(source_obj, target_name, overwrite, True)
 
     def portable_manifest_text(self, stream_name="."):


@@ -897,7 +985,8 @@ class RichCollectionBase(CollectionBase):
         return self._get_manifest_text(stream_name, True, True)
 
     @synchronized
         return self._get_manifest_text(stream_name, True, True)
 
     @synchronized

-    def manifest_text(self, stream_name=".", strip=False, normalize=False):
+    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
         """Get the manifest text for this collection, sub collections and files.
 
         This method will flush outstanding blocks to Keep.  By default, it will


@@ -916,13 +1005,18 @@ class RichCollectionBase(CollectionBase):
           is not modified, return the original manifest text even if it is not
           in normalized form.
 
           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.
+

         """
 
         """
 

-        self._my_block_manager().commit_all()
-        return self._get_manifest_text(stream_name, strip, normalize)
+        if not only_committed:
+            self._my_block_manager().commit_all()
+        return self._get_manifest_text(stream_name, strip, normalize,
+                                       only_committed=only_committed)

 
     @synchronized
 
     @synchronized

-    def _get_manifest_text(self, stream_name, strip, normalize):
+    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:
         """Get the manifest text for this collection, sub collections and files.
 
         :stream_name:


@@ -938,6 +1032,9 @@ class RichCollectionBase(CollectionBase):
           is not modified, return the original manifest text even if it is not
           in normalized form.
 
           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:
         """
 
         if not self.committed() or self._manifest_text is None or normalize:


@@ -951,6 +1048,8 @@ class RichCollectionBase(CollectionBase):
                 for segment in arvfile.segments():
                     loc = segment.locator
                     if arvfile.parent._my_block_manager().is_bufferblock(loc):
                 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()
                         loc = arvfile.parent._my_block_manager().get_bufferblock(loc).locator()
                     if strip:
                         loc = KeepLocator(loc).stripped()


@@ -960,7 +1059,9 @@ class RichCollectionBase(CollectionBase):
             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)]:
             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))
+                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 "".join(buf)
         else:
             if strip:


@@ -968,6 +1069,24 @@ class RichCollectionBase(CollectionBase):
             else:
                 return self._manifest_text
 
             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.
     @synchronized
     def diff(self, end_collection, prefix=".", holding_collection=None):
         """Generate list of add/modify/delete actions.


@@ -1003,7 +1122,7 @@ class RichCollectionBase(CollectionBase):
 
         """
         if changes:
 
         """
         if changes:

-            self._committed = False
+            self.set_committed(False)

         for change in changes:
             event_type = change[0]
             path = change[1]
         for change in changes:
             event_type = change[0]
             path = change[1]


@@ -1044,8 +1163,13 @@ class RichCollectionBase(CollectionBase):
 
     def portable_data_hash(self):
         """Get the portable data hash for this collection's manifest."""
 
     def portable_data_hash(self):
         """Get the portable data hash for this collection's manifest."""

-        stripped = self.portable_manifest_text()
-        return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
+        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):
 
     @synchronized
     def subscribe(self, callback):


@@ -1086,7 +1210,7 @@ class RichCollectionBase(CollectionBase):
     @synchronized
     def flush(self):
         """Flush bufferblocks to Keep."""
     @synchronized
     def flush(self):
         """Flush bufferblocks to Keep."""

-        for e in self.values():
+        for e in listvalues(self):

             e.flush()
 
 
             e.flush()
 
 


@@ -1135,32 +1259,47 @@ class Collection(RichCollectionBase):
                  num_retries=None,
                  parent=None,
                  apiconfig=None,
                  num_retries=None,
                  parent=None,
                  apiconfig=None,

-                 block_manager=None):
+                 block_manager=None,
+                 replication_desired=None,
+                 put_threads=None):

         """Collection constructor.
 
         :manifest_locator_or_text:
         """Collection constructor.
 
         :manifest_locator_or_text:

-          One of Arvados collection UUID, block locator of
-          a manifest, raw manifest text, or None (to create an empty collection).
+          An Arvados collection UUID, portable data hash, raw manifest
+          text, or (if creating an empty collection) None.
+

         :parent:
           the parent Collection, may be 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.
         :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`.
         :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`.
         :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.
         :num_retries:
           the number of retries for API and Keep requests.

+

         :block_manager:
           the block manager to use.  If not specified, create one.
 
         :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.
+

         """
         super(Collection, self).__init__(parent)
         self._api_client = api_client
         self._keep_client = keep_client
         self._block_manager = block_manager
         """
         super(Collection, self).__init__(parent)
         self._api_client = api_client
         self._keep_client = keep_client
         self._block_manager = block_manager

+        self.replication_desired = replication_desired
+        self.put_threads = put_threads

 
         if apiconfig:
             self._config = apiconfig
 
         if apiconfig:
             self._config = apiconfig


@@ -1170,6 +1309,7 @@ class Collection(RichCollectionBase):
         self.num_retries = num_retries if num_retries is not None else 0
         self._manifest_locator = None
         self._manifest_text = None
         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._api_response = None
         self._past_versions = set()
 


@@ -1177,12 +1317,16 @@ class Collection(RichCollectionBase):
         self.events = None
 
         if manifest_locator_or_text:
         self.events = None
 
         if manifest_locator_or_text:

-            if re.match(util.keep_locator_pattern, manifest_locator_or_text):
+            if re.match(arvados.util.keep_locator_pattern, manifest_locator_or_text):

                 self._manifest_locator = manifest_locator_or_text
                 self._manifest_locator = manifest_locator_or_text

-            elif re.match(util.collection_uuid_pattern, manifest_locator_or_text):
+            elif re.match(arvados.util.collection_uuid_pattern, manifest_locator_or_text):

                 self._manifest_locator = manifest_locator_or_text
                 self._manifest_locator = manifest_locator_or_text

-            elif re.match(util.manifest_pattern, 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
                 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")
             else:
                 raise errors.ArgumentError(
                     "Argument to CollectionReader is not a manifest or a collection UUID")


@@ -1195,6 +1339,21 @@ class Collection(RichCollectionBase):
     def root_collection(self):
         return self
 
     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 stream_name(self):
         return "."
 


@@ -1232,7 +1391,8 @@ class Collection(RichCollectionBase):
     def _my_api(self):
         if self._api_client is None:
             self._api_client = ThreadSafeApiCache(self._config)
     def _my_api(self):
         if self._api_client is None:
             self._api_client = ThreadSafeApiCache(self._config)

-            self._keep_client = self._api_client.keep
+            if self._keep_client is None:
+                self._keep_client = self._api_client.keep

         return self._api_client
 
     @synchronized
         return self._api_client
 
     @synchronized


@@ -1247,7 +1407,10 @@ class Collection(RichCollectionBase):
     @synchronized
     def _my_block_manager(self):
         if self._block_manager is None:
     @synchronized
     def _my_block_manager(self):
         if self._block_manager is None:

-            self._block_manager = _BlockManager(self._my_keep())
+            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)

         return self._block_manager
 
     def _remember_api_response(self, response):
         return self._block_manager
 
     def _remember_api_response(self, response):


@@ -1262,62 +1425,31 @@ class Collection(RichCollectionBase):
         # 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.
         # 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._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']
-            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
+        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 from the API server
+        if self.replication_desired is None:
+            self.replication_desired = self._api_response.get('replication_desired', None)

 
     def _populate(self):
 
     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:
         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 errors.NotFoundError(
-                ("Failed to retrieve collection '{}' " +
-                 "from either API server ({}) or Keep ({})."
-                 ).format(
-                    self._manifest_locator,
-                    error_via_api,
-                    error_via_keep))
-        # populate
+            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)
 
         self._baseline_manifest = self._manifest_text
         self._import_manifest(self._manifest_text)
 

-

     def _has_collection_uuid(self):
     def _has_collection_uuid(self):

-        return self._manifest_locator is not None and re.match(util.collection_uuid_pattern, self._manifest_locator)
+        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 __enter__(self):
         return self


@@ -1393,17 +1525,34 @@ class Collection(RichCollectionBase):
     @must_be_writable
     @synchronized
     @retry_method
     @must_be_writable
     @synchronized
     @retry_method

-    def save(self, merge=True, num_retries=None):
+    def save(self,
+             properties=None,
+             storage_classes=None,
+             trash_at=None,
+             merge=True,
+             num_retries=None):

         """Save collection to an existing collection record.
 
         Commit pending buffer blocks to Keep, merge with remote record (if
         """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
+        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()`.
 
         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.
         :merge:
           Update and merge remote changes before saving.  Otherwise, any
           remote changes will be ignored and overwritten.


@@ -1412,9 +1561,33 @@ class Collection(RichCollectionBase):
           Retry count on API calls (if None,  use the collection default)
 
         """
           Retry count on API calls (if None,  use the collection default)
 
         """

+        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.")
+
+        body={}
+        if properties:
+            body["properties"] = properties
+        if storage_classes:
+            body["storage_classes_desired"] = storage_classes
+        if trash_at:
+            t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ")
+            body["trash_at"] = t
+

         if not self.committed():
         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.")
             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()
 
 
             self._my_block_manager().commit_all()
 


@@ -1422,13 +1595,20 @@ class Collection(RichCollectionBase):
                 self.update()
 
             text = self.manifest_text(strip=False)
                 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,
             self._remember_api_response(self._my_api().collections().update(
                 uuid=self._manifest_locator,

-                body={'manifest_text': text}
-                ).execute(
-                    num_retries=num_retries))
+                body=body
+                ).execute(num_retries=num_retries))

             self._manifest_text = self._api_response["manifest_text"]
             self._manifest_text = self._api_response["manifest_text"]

-            self.set_committed()
+            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
 
 
         return self._manifest_text
 


@@ -1439,15 +1619,17 @@ class Collection(RichCollectionBase):
     def save_new(self, name=None,
                  create_collection_record=True,
                  owner_uuid=None,
     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,
                  ensure_unique_name=False,

-                 num_retries=None,
-                 replication_desired=None):
+                 num_retries=None):

         """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
         """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.
+        the new record used by `save()`. Returns the current manifest text.

 
         :name:
           The collection name.
 
         :name:
           The collection name.


@@ -1460,6 +1642,18 @@ class Collection(RichCollectionBase):
           the user, or project uuid that will own this collection.
           If None, defaults to the current user.
 
           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
         :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


@@ -1468,40 +1662,60 @@ class Collection(RichCollectionBase):
         :num_retries:
           Retry count on API calls (if None,  use the collection default)
 
         :num_retries:
           Retry count on API calls (if None,  use the collection default)
 

-        :replication_desired:
-          How many copies should Arvados maintain. If None, API server default
-          configuration applies.
-

         """
         """

+        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 self._has_remote_blocks:
+            # Copy any remote blocks to the local cluster.
+            self._copy_remote_blocks(remote_blocks={})
+            self._has_remote_blocks = False
+

         self._my_block_manager().commit_all()
         text = self.manifest_text(strip=False)
 
         if create_collection_record:
         self._my_block_manager().commit_all()
         text = self.manifest_text(strip=False)
 
         if create_collection_record:

-            replication_attr = 'replication_desired'
-            if self._my_api()._schema.schemas['Collection']['properties'].get(replication_attr, None) is None:
-                # API called it 'redundancy' before #3410.
-                replication_attr = 'redundancy'
-

             if name is None:
                 name = "New collection"
                 ensure_unique_name = True
 
             body = {"manifest_text": text,
                     "name": name,
             if name is None:
                 name = "New collection"
                 ensure_unique_name = True
 
             body = {"manifest_text": text,
                     "name": name,

-                    replication_attr: replication_desired}
+                    "replication_desired": self.replication_desired}

             if owner_uuid:
                 body["owner_uuid"] = owner_uuid
             if owner_uuid:
                 body["owner_uuid"] = owner_uuid

+            if properties:
+                body["properties"] = properties
+            if storage_classes:
+                body["storage_classes_desired"] = storage_classes
+            if trash_at:
+                t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ")
+                body["trash_at"] = t

 
             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._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._manifest_text = text

-            self.set_committed()
+            self.set_committed(True)

 
         return text
 
 
         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`.
     @synchronized
     def _import_manifest(self, manifest_text):
         """Import a manifest into a `Collection`.


@@ -1520,41 +1734,46 @@ class Collection(RichCollectionBase):
         stream_name = None
         state = STREAM_NAME
 
         stream_name = None
         state = STREAM_NAME
 

-        for token_and_separator in re.finditer(r'(\S+)(\s+|$)', manifest_text):
+        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
             tok = token_and_separator.group(1)
             sep = token_and_separator.group(2)
 
             if state == STREAM_NAME:
                 # starting a new stream

-                stream_name = tok.replace('\\040', ' ')
+                stream_name = self._unescape_manifest_path(tok)

                 blocks = []
                 segments = []
                 blocks = []
                 segments = []

-                streamoffset = 0L
+                streamoffset = 0

                 state = BLOCKS
                 self.find_or_create(stream_name, COLLECTION)
                 continue
 
             if state == BLOCKS:
                 state = BLOCKS
                 self.find_or_create(stream_name, COLLECTION)
                 continue
 
             if state == BLOCKS:

-                block_locator = re.match(r'[0-9a-f]{32}\+(\d+)(\+\S+)*', tok)
+                block_locator = self._block_re.match(tok)

                 if block_locator:
                 if block_locator:

-                    blocksize = long(block_locator.group(1))
+                    blocksize = int(block_locator.group(1))

                     blocks.append(Range(tok, streamoffset, blocksize, 0))
                     streamoffset += blocksize
                 else:
                     state = SEGMENTS
 
             if state == SEGMENTS:
                     blocks.append(Range(tok, streamoffset, blocksize, 0))
                     streamoffset += blocksize
                 else:
                     state = SEGMENTS
 
             if state == SEGMENTS:

-                file_segment = re.search(r'^(\d+):(\d+):(\S+)', tok)
+                file_segment = self._segment_re.match(tok)

                 if file_segment:
                 if file_segment:

-                    pos = long(file_segment.group(1))
-                    size = long(file_segment.group(2))
-                    name = file_segment.group(3).replace('\\040', ' ')
-                    filepath = os.path.join(stream_name, name)
-                    afile = self.find_or_create(filepath, FILE)
-                    if isinstance(afile, ArvadosFile):
-                        afile.add_segment(blocks, pos, size)
+                    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:
                     else:

-                        raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath)
+                        filepath = os.path.join(stream_name, name)
+                        afile = self.find_or_create(filepath, FILE)
+                        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)
                 else:
                     # error!
                     raise errors.SyntaxError("Invalid manifest format, expected file segment but did not match format: '%s'" % tok)


@@ -1563,7 +1782,7 @@ class Collection(RichCollectionBase):
                 stream_name = None
                 state = STREAM_NAME
 
                 stream_name = None
                 state = STREAM_NAME
 

-        self.set_committed()
+        self.set_committed(True)

 
     @synchronized
     def notify(self, event, collection, name, item):
 
     @synchronized
     def notify(self, event, collection, name, item):


@@ -1613,20 +1832,29 @@ class Subcollection(RichCollectionBase):
     @must_be_writable
     @synchronized
     def _reparent(self, newparent, newname):
     @must_be_writable
     @synchronized
     def _reparent(self, newparent, newname):

-        self._committed = False
+        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
 
         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)
+

 
 class CollectionReader(Collection):
     """A read-only collection object.
 
 
 class CollectionReader(Collection):
     """A read-only collection object.
 

-    Initialize from an api collection record locator, a portable data hash of a
-    manifest, or raw manifest text.  See `Collection` constructor for detailed
-    options.
+    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):
 
     """
     def __init__(self, manifest_locator_or_text, *args, **kwargs):