Merge branch 'master' into 3198-writable-fuse

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

diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py
index a77f3093f8a7d682f674f9fb80f8653f558516a1..89cbda937c59fbb5064d9c81644b07dba623f806 100644 (file)
--- a/sdk/python/arvados/collection.py
+++ b/sdk/python/arvados/collection.py
@@ -10,7 +10,7 @@ import threading
 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, SYNC_READONLY, SYNC_EXPLICIT, NoopLock
+from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, _BlockManager, synchronized, must_be_writable, NoopLock

 from keep import KeepLocator, KeepClient
 from .stream import StreamReader
 from ._normalize_stream import normalize_stream
 from keep import KeepLocator, KeepClient
 from .stream import StreamReader
 from ._normalize_stream import normalize_stream


@@ -38,7 +38,8 @@ class CollectionBase(object):
         return self._keep_client
 
     def stripped_manifest(self):
         return self._keep_client
 
     def stripped_manifest(self):

-        """
+        """Get the manifest with locator hints stripped.
+

         Return the manifest for the current collection with all
         non-portable hints (i.e., permission signatures and other
         hints other than size hints) removed from the locators.
         Return the manifest for the current collection with all
         non-portable hints (i.e., permission signatures and other
         hints other than size hints) removed from the locators.


@@ -469,13 +470,14 @@ class ResumableCollectionWriter(CollectionWriter):
                 "resumable writer can't accept unsourced data")
         return super(ResumableCollectionWriter, self).write(data)
 
                 "resumable writer can't accept unsourced data")
         return super(ResumableCollectionWriter, self).write(data)
 

+

 ADD = "add"
 DEL = "del"
 MOD = "mod"
 FILE = "file"
 COLLECTION = "collection"
 
 ADD = "add"
 DEL = "del"
 MOD = "mod"
 FILE = "file"
 COLLECTION = "collection"
 

-class SynchronizedCollectionBase(CollectionBase):
+class RichCollectionBase(CollectionBase):

     """Base class for Collections and Subcollections.
 
     Implements the majority of functionality relating to accessing items in the
     """Base class for Collections and Subcollections.
 
     Implements the majority of functionality relating to accessing items in the


@@ -486,6 +488,7 @@ class SynchronizedCollectionBase(CollectionBase):
     def __init__(self, parent=None):
         self.parent = parent
         self._modified = True
     def __init__(self, parent=None):
         self.parent = parent
         self._modified = True

+        self._callback = None

         self._items = {}
 
     def _my_api(self):
         self._items = {}
 
     def _my_api(self):


@@ -497,7 +500,7 @@ class SynchronizedCollectionBase(CollectionBase):
     def _my_block_manager(self):
         raise NotImplementedError()
 
     def _my_block_manager(self):
         raise NotImplementedError()
 

-    def sync_mode(self):
+    def writable(self):

         raise NotImplementedError()
 
     def root_collection(self):
         raise NotImplementedError()
 
     def root_collection(self):


@@ -520,26 +523,24 @@ class SynchronizedCollectionBase(CollectionBase):
         the path.
 
         :create_type:
         the path.
 
         :create_type:

-          One of `arvado.collection.FILE` or
-          `arvado.collection.COLLECTION`.  If the path is not found, and value
+          One of `arvados.collection.FILE` or
+          `arvados.collection.COLLECTION`.  If the path is not found, and value

           of create_type is FILE then create and return a new ArvadosFile for
           the last path component.  If COLLECTION, then create and return a new
           Collection for the last path component.
 
         """
 
           of create_type is FILE then create and return a new ArvadosFile for
           the last path component.  If COLLECTION, then create and return a new
           Collection for the last path component.
 
         """
 

-        pathcomponents = path.split("/")
-
-        if pathcomponents and pathcomponents[0]:
+        pathcomponents = path.split("/", 1)
+        if pathcomponents[0]:

             item = self._items.get(pathcomponents[0])
             if len(pathcomponents) == 1:
             item = self._items.get(pathcomponents[0])
             if len(pathcomponents) == 1:

-                # item must be a file

                 if item is None:
                     # create new file
                     if create_type == COLLECTION:
                 if item is None:
                     # create new file
                     if create_type == COLLECTION:

-                        item = Subcollection(self)
+                        item = Subcollection(self, pathcomponents[0])

                     else:
                     else:

-                        item = ArvadosFile(self)
+                        item = ArvadosFile(self, pathcomponents[0])

                     self._items[pathcomponents[0]] = item
                     self._modified = True
                     self.notify(ADD, self, pathcomponents[0], item)
                     self._items[pathcomponents[0]] = item
                     self._modified = True
                     self.notify(ADD, self, pathcomponents[0], item)


@@ -547,15 +548,14 @@ class SynchronizedCollectionBase(CollectionBase):
             else:
                 if item is None:
                     # create new collection
             else:
                 if item is None:
                     # create new collection

-                    item = Subcollection(self)
+                    item = Subcollection(self, pathcomponents[0])

                     self._items[pathcomponents[0]] = item
                     self._modified = True
                     self.notify(ADD, self, pathcomponents[0], item)
                     self._items[pathcomponents[0]] = item
                     self._modified = True
                     self.notify(ADD, self, pathcomponents[0], item)

-                del pathcomponents[0]
-                if isinstance(item, SynchronizedCollectionBase):
-                    return item.find_or_create("/".join(pathcomponents), create_type)
+                if isinstance(item, RichCollectionBase):
+                    return item.find_or_create(pathcomponents[1], create_type)

                 else:
                 else:

-                    raise IOError((errno.ENOTDIR, "Interior path components must be subcollection"))
+                    raise IOError(errno.ENOTDIR, "Interior path components must be subcollection")

         else:
             return self
 
         else:
             return self
 


@@ -567,23 +567,23 @@ class SynchronizedCollectionBase(CollectionBase):
         found.
 
         """
         found.
 
         """

-        pathcomponents = path.split("/")
+        if not path:
+            raise errors.ArgumentError("Parameter 'path' must not be empty.")

 
 

-        if pathcomponents and pathcomponents[0]:
-            item = self._items.get(pathcomponents[0])
-            if len(pathcomponents) == 1:
-                # item must be a file
-                return item
-            else:
-                del pathcomponents[0]
-                if isinstance(item, SynchronizedCollectionBase):
-                    return item.find("/".join(pathcomponents))
-                else:
-                    raise IOError((errno.ENOTDIR, "Interior path components must be subcollection"))
+        pathcomponents = path.split("/", 1)
+        item = self._items.get(pathcomponents[0])
+        if len(pathcomponents) == 1:
+            return item

         else:
         else:

-            return self
+            if isinstance(item, RichCollectionBase):
+                if pathcomponents[1]:
+                    return item.find(pathcomponents[1])
+                else:
+                    return item
+            else:
+                raise IOError(errno.ENOTDIR, "Interior path components must be subcollection")

 
 

-    def mkdirs(path):
+    def mkdirs(self, path):

         """Recursive subcollection create.
 
         Like `os.mkdirs()`.  Will create intermediate subcollections needed to
         """Recursive subcollection create.
 
         Like `os.mkdirs()`.  Will create intermediate subcollections needed to


@@ -615,8 +615,8 @@ class SynchronizedCollectionBase(CollectionBase):
             raise errors.ArgumentError("Bad mode '%s'" % mode)
         create = (mode != "r")
 
             raise errors.ArgumentError("Bad mode '%s'" % mode)
         create = (mode != "r")
 

-        if create and self.sync_mode() == SYNC_READONLY:
-            raise IOError((errno.EROFS, "Collection is read only"))
+        if create and not self.writable():
+            raise IOError(errno.EROFS, "Collection is read only")

 
         if create:
             arvfile = self.find_or_create(path, FILE)
 
         if create:
             arvfile = self.find_or_create(path, FILE)


@@ -624,9 +624,9 @@ class SynchronizedCollectionBase(CollectionBase):
             arvfile = self.find(path)
 
         if arvfile is None:
             arvfile = self.find(path)
 
         if arvfile is None:

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

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

-            raise IOError((errno.EISDIR, "Path must refer to a file."))
+            raise IOError(errno.EISDIR, "Path must refer to a file.")

 
         if mode[0] == "w":
             arvfile.truncate(0)
 
         if mode[0] == "w":
             arvfile.truncate(0)


@@ -634,14 +634,13 @@ class SynchronizedCollectionBase(CollectionBase):
         name = os.path.basename(path)
 
         if mode == "r":
         name = os.path.basename(path)
 
         if mode == "r":

-            return ArvadosFileReader(arvfile, name, mode, num_retries=self.num_retries)
+            return ArvadosFileReader(arvfile, mode, num_retries=self.num_retries)

         else:
         else:

-            return ArvadosFileWriter(arvfile, name, mode, num_retries=self.num_retries)
+            return ArvadosFileWriter(arvfile, mode, num_retries=self.num_retries)

 
     @synchronized
     def modified(self):
 
     @synchronized
     def modified(self):

-        """Test if the collection (or any subcollection or file) has been modified
-        since it was created."""
+        """Test if the collection (or any subcollection or file) has been modified."""

         if self._modified:
             return True
         for k,v in self._items.items():
         if self._modified:
             return True
         for k,v in self._items.items():


@@ -661,22 +660,18 @@ class SynchronizedCollectionBase(CollectionBase):
         """Iterate over names of files and collections contained in this collection."""
         return iter(self._items.keys())
 
         """Iterate over names of files and collections contained in this collection."""
         return iter(self._items.keys())
 

-    @synchronized
-    def iterkeys(self):
-        """Iterate over names of files and collections directly contained in this collection."""
-        return self._items.keys()
-

     @synchronized
     def __getitem__(self, k):
     @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.
+        """Get a file or collection that is directly contained by this collection.
+
+        If you want to search a path, use `find()` instead.
+

         """
         return self._items[k]
 
     @synchronized
     def __contains__(self, k):
         """
         return self._items[k]
 
     @synchronized
     def __contains__(self, k):

-        """If there is a file or collection a directly contained by this collection
-        with name `k`."""
+        """Test if there is a file or collection a directly contained by this collection."""

         return k in self._items
 
     @synchronized
         return k in self._items
 
     @synchronized


@@ -709,7 +704,7 @@ class SynchronizedCollectionBase(CollectionBase):
 
     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`."""

-        return self.find(path) != None
+        return self.find(path) is not None

 
     @must_be_writable
     @synchronized
 
     @must_be_writable
     @synchronized


@@ -719,60 +714,84 @@ class SynchronizedCollectionBase(CollectionBase):
         :recursive:
           Specify whether to remove non-empty subcollections (True), or raise an error (False).
         """
         :recursive:
           Specify whether to remove non-empty subcollections (True), or raise an error (False).
         """

-        pathcomponents = path.split("/")

 
 

-        if len(pathcomponents) > 0:
-            item = self._items.get(pathcomponents[0])
-            if item is None:
-                raise IOError((errno.ENOENT, "File not found"))
-            if len(pathcomponents) == 1:
-                if isinstance(self._items[pathcomponents[0]], SynchronizedCollectionBase) and len(self._items[pathcomponents[0]]) > 0 and not recursive:
-                    raise IOError((errno.ENOTEMPTY, "Subcollection not empty"))
-                deleteditem = self._items[pathcomponents[0]]
-                del self._items[pathcomponents[0]]
-                self._modified = True
-                self.notify(DEL, self, pathcomponents[0], deleteditem)
-            else:
-                del pathcomponents[0]
-                item.remove("/".join(pathcomponents))
+        if not path:
+            raise errors.ArgumentError("Parameter 'path' must not be empty.")
+
+        pathcomponents = path.split("/", 1)
+        item = self._items.get(pathcomponents[0])
+        if item is None:
+            raise IOError(errno.ENOENT, "File not found")
+        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")
+            deleteditem = self._items[pathcomponents[0]]
+            del self._items[pathcomponents[0]]
+            self._modified = True
+            self.notify(DEL, self, pathcomponents[0], deleteditem)

         else:
         else:

-            raise IOError((errno.ENOENT, "File not found"))
+            item.remove(pathcomponents[1])

 
 

-    def _cloneinto(self, target):
-        for k,v in self._items.items():
-            target._items[k] = v.clone(target)
+    def _clonefrom(self, source):
+        for k,v in source.items():
+            self._items[k] = v.clone(self, k)

 
     def clone(self):
         raise NotImplementedError()
 
     @must_be_writable
     @synchronized
 
     def clone(self):
         raise NotImplementedError()
 
     @must_be_writable
     @synchronized

-    def copy(self, source, target_path, source_collection=None, overwrite=False):
-        """Copy a file or subcollection to a new path in this collection.
+    def add(self, source_obj, target_name, overwrite=False, reparent=False):
+        """Copy or move a file or subcollection to this collection.

 
 

-        :source:
-          An ArvadosFile, Subcollection, or string with a path to source file or subcollection
+        :source_obj:
+          An ArvadosFile, or Subcollection object

 
 

-        :target_path:
-          Destination file or path.  If the target path already exists and is a
-          subcollection, the item will be placed inside the subcollection.  If
-          the target path already exists and is a file, this will raise an error
-          unless you specify `overwrite=True`.
-
-        :source_collection:
-          Collection to copy `source_path` from (default `self`)
+        :target_name:
+          Destination item name.  If the target name already exists and is a
+          file, this will raise an error unless you specify `overwrite=True`.

 
         :overwrite:
           Whether to overwrite target file if it already exists.
 
         :overwrite:
           Whether to overwrite target file if it already exists.

+
+        :reparent:
+          If True, source_obj will be moved from its parent collection to this collection.
+          If False, source_obj will be copied and the parent collection will be
+          unmodified.
+

         """
         """

+
+        if target_name in self and not overwrite:
+            raise IOError(errno.EEXIST, "File already exists")
+
+        modified_from = None
+        if target_name in self:
+            modified_from = self[target_name]
+
+        # Actually make the move or copy.
+        if reparent:
+            source_obj.reparent(self, target_name)
+            item = source_obj
+        else:
+            item = source_obj.clone(self, target_name)
+
+        self._items[target_name] = item
+        self._modified = True
+
+        if modified_from:
+            self.notify(MOD, self, target_name, (modified_from, item))
+        else:
+            self.notify(ADD, self, target_name, item)
+
+    def _get_src_target(self, source, target_path, source_collection, create_dest):

         if source_collection is None:
             source_collection = self
 
         if source_collection is None:
             source_collection = self
 

-        # Find the object to copy
+        # Find the object

         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")

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


@@ -782,40 +801,120 @@ class SynchronizedCollectionBase(CollectionBase):
         targetcomponents = target_path.split("/")
 
         # Determine the name to use.
         targetcomponents = target_path.split("/")
 
         # Determine the name to use.

-        target_name = targetcomponents[-1] if targetcomponents[-1] else (sourcecomponents[-1] if sourcecomponents else None)
+        target_name = targetcomponents[-1] if targetcomponents[-1] else sourcecomponents[-1]

 
         if not target_name:
             raise errors.ArgumentError("Target path is empty and source is an object.  Cannot determine destination filename to use.")
 
 
         if not target_name:
             raise errors.ArgumentError("Target path is empty and source is an object.  Cannot determine destination filename to use.")
 

-        target_dir = self.find_or_create("/".join(targetcomponents[0:-1]), COLLECTION)
+        if create_dest:
+            target_dir = self.find_or_create("/".join(targetcomponents[0:-1]), COLLECTION)
+        else:
+            if len(targetcomponents) > 1:
+                target_dir = self.find("/".join(targetcomponents[0:-1]))
+            else:
+                target_dir = self

 
 

-        if target_name in target_dir:
-            if isinstance(target_dir[target_name], SynchronizedCollectionBase) and sourcecomponents:
-                target_dir = target_dir[target_name]
-                target_name = sourcecomponents[-1]
-            elif not overwrite:
-                raise IOError((errno.EEXIST, "File already exists"))
+        if target_dir is None:
+            raise IOError(errno.ENOENT, "Target directory not found.")

 
 

-        modified_from = None
-        if target_name in target_dir:
-            modified_from = target_dir[target_name]
+        if target_name in target_dir and isinstance(self[target_name], RichCollectionBase) and sourcecomponents:
+            target_dir = target_dir[target_name]
+            target_name = sourcecomponents[-1]

 
 

-        # Actually make the copy.
-        dup = source_obj.clone(target_dir)
-        target_dir._items[target_name] = dup
-        target_dir._modified = True
+        return (source_obj, target_dir, target_name)

 
 

-        if modified_from:
-            self.notify(MOD, target_dir, target_name, (modified_from, dup))
-        else:
-            self.notify(ADD, target_dir, target_name, dup)
+    @must_be_writable
+    @synchronized
+    def copy(self, source, target_path, source_collection=None, overwrite=False):
+        """Copy a file or subcollection to a new path in this collection.
+
+        :source:
+          A string with a path to source file or subcollection, or an actual ArvadosFile or Subcollection object.
+
+        :target_path:
+          Destination file or path.  If the target path already exists and is a
+          subcollection, the item will be placed inside the subcollection.  If
+          the target path already exists and is a file, this will raise an error
+          unless you specify `overwrite=True`.
+
+        :source_collection:
+          Collection to copy `source_path` from (default `self`)

 
 

+        :overwrite:
+          Whether to overwrite target file if it already exists.
+        """
+
+        source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, True)
+        target_dir.add(source_obj, target_name, overwrite, False)
+
+    @must_be_writable

     @synchronized
     @synchronized

+    def rename(self, source, target_path, source_collection=None, overwrite=False):
+        """Move a file or subcollection from `source_collection` to a new path in this collection.
+
+        :source:
+          A string with a path to source file or subcollection.
+
+        :target_path:
+          Destination file or path.  If the target path already exists and is a
+          subcollection, the item will be placed inside the subcollection.  If
+          the target path already exists and is a file, this will raise an error
+          unless you specify `overwrite=True`.
+
+        :source_collection:
+          Collection to copy `source_path` from (default `self`)
+
+        :overwrite:
+          Whether to overwrite target file if it already exists.
+        """
+
+        source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, False)
+        if not source_obj.writable():
+            raise IOError(errno.EROFS, "Source collection must be writable.")
+        target_dir.add(source_obj, target_name, overwrite, True)
+
+    def portable_manifest_text(self, stream_name="."):
+        """Get the manifest text for this collection, sub collections and files.
+
+        This method does not flush outstanding blocks to Keep.  It will return
+        a normalized manifest with access tokens stripped.
+
+        :stream_name:
+          Name to use for this stream (directory)
+
+        """
+        return self._get_manifest_text(stream_name, True, True)
+

     def manifest_text(self, stream_name=".", strip=False, normalize=False):
         """Get the manifest text for this collection, sub collections and files.
 
     def manifest_text(self, stream_name=".", strip=False, normalize=False):
         """Get the manifest text for this collection, sub collections and files.
 

+        This method will flush outstanding blocks to Keep.  By default, it will
+        not normalize an unmodified manifest or strip access tokens.
+

         :stream_name:
         :stream_name:

-          Name of the stream (directory)
+          Name to use for this stream (directory)
+
+        :strip:
+          If True, remove signing tokens from block locators if present.
+          If False (default), block locators are left unchanged.
+
+        :normalize:
+          If True, always export the manifest text in normalized form
+          even if the Collection is not modified.  If False (default) and the collection
+          is not modified, return the original manifest text even if it is not
+          in normalized form.
+
+        """
+
+        self._my_block_manager().commit_all()
+        return self._get_manifest_text(stream_name, strip, normalize)
+
+    @synchronized
+    def _get_manifest_text(self, stream_name, strip, normalize):
+        """Get the manifest text for this collection, sub collections and files.
+
+        :stream_name:
+          Name to use for this stream (directory)

 
         :strip:
           If True, remove signing tokens from block locators if present.
 
         :strip:
           If True, remove signing tokens from block locators if present.


@@ -830,13 +929,12 @@ class SynchronizedCollectionBase(CollectionBase):
         """
 
         if self.modified() or self._manifest_text is None or normalize:
         """
 
         if self.modified() or self._manifest_text is None or normalize:

-            item  = self

             stream = {}
             stream = {}

-            buf = ""
-            sorted_keys = sorted(item.keys())
-            for filename in [s for s in sorted_keys if isinstance(item[s], ArvadosFile)]:
+            buf = []
+            sorted_keys = sorted(self.keys())
+            for filename in [s for s in sorted_keys if isinstance(self[s], ArvadosFile)]:

                 # Create a stream per file `k`
                 # Create a stream per file `k`

-                arvfile = item[filename]
+                arvfile = self[filename]

                 filestream = []
                 for segment in arvfile.segments():
                     loc = segment.locator
                 filestream = []
                 for segment in arvfile.segments():
                     loc = segment.locator


@@ -848,11 +946,10 @@ class SynchronizedCollectionBase(CollectionBase):
                                          segment.segment_offset, segment.range_size))
                 stream[filename] = filestream
             if stream:
                                          segment.segment_offset, segment.range_size))
                 stream[filename] = filestream
             if stream:

-                buf += ' '.join(normalize_stream(stream_name, stream))
-                buf += "\n"
-            for dirname in [s for s in sorted_keys if isinstance(item[s], SynchronizedCollectionBase)]:
-                buf += item[dirname].manifest_text(stream_name=os.path.join(stream_name, dirname), strip=strip)
-            return buf
+                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))
+            return "".join(buf)

         else:
             if strip:
                 return self.stripped_manifest()
         else:
             if strip:
                 return self.stripped_manifest()


@@ -861,24 +958,25 @@ class SynchronizedCollectionBase(CollectionBase):
 
     @synchronized
     def diff(self, end_collection, prefix=".", holding_collection=None):
 
     @synchronized
     def diff(self, end_collection, prefix=".", holding_collection=None):

-        """
-        Generate list of add/modify/delete actions which, when given to `apply`, will
-        change `self` to match `end_collection`
+        """Generate list of add/modify/delete actions.
+
+        When given to `apply`, will change `self` to match `end_collection`
+

         """
         changes = []
         if holding_collection is None:
             holding_collection = Collection(api_client=self._my_api(), keep_client=self._my_keep())
         for k in self:
             if k not in end_collection:
         """
         changes = []
         if holding_collection is None:
             holding_collection = Collection(api_client=self._my_api(), keep_client=self._my_keep())
         for k in self:
             if k not in end_collection:

-               changes.append((DEL, os.path.join(prefix, k), self[k].clone(holding_collection)))
+               changes.append((DEL, os.path.join(prefix, k), self[k].clone(holding_collection, "")))

         for k in end_collection:
             if k in self:
                 if isinstance(end_collection[k], Subcollection) and isinstance(self[k], Subcollection):
                     changes.extend(self[k].diff(end_collection[k], os.path.join(prefix, k), holding_collection))
                 elif end_collection[k] != self[k]:
         for k in end_collection:
             if k in self:
                 if isinstance(end_collection[k], Subcollection) and isinstance(self[k], Subcollection):
                     changes.extend(self[k].diff(end_collection[k], os.path.join(prefix, k), holding_collection))
                 elif end_collection[k] != self[k]:

-                    changes.append((MOD, os.path.join(prefix, k), self[k].clone(holding_collection), end_collection[k].clone(holding_collection)))
+                    changes.append((MOD, os.path.join(prefix, k), self[k].clone(holding_collection, ""), end_collection[k].clone(holding_collection, "")))

             else:
             else:

-                changes.append((ADD, os.path.join(prefix, k), end_collection[k].clone(holding_collection)))
+                changes.append((ADD, os.path.join(prefix, k), end_collection[k].clone(holding_collection, "")))

         return changes
 
     @must_be_writable
         return changes
 
     @must_be_writable


@@ -930,14 +1028,32 @@ class SynchronizedCollectionBase(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.manifest_text(strip=True)
+        stripped = self.portable_manifest_text()

         return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
 
         return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
 

+    @synchronized
+    def subscribe(self, callback):
+        if self._callback is None:
+            self._callback = callback
+        else:
+            raise errors.ArgumentError("A callback is already set on this collection.")
+
+    @synchronized
+    def unsubscribe(self):
+        if self._callback is not None:
+            self._callback = None
+
+    @synchronized
+    def notify(self, event, collection, name, item):
+        if self._callback:
+            self._callback(event, collection, name, item)
+        self.root_collection().notify(event, collection, name, item)
+

     @synchronized
     def __eq__(self, other):
         if other is self:
             return True
     @synchronized
     def __eq__(self, other):
         if other is self:
             return True

-        if not isinstance(other, SynchronizedCollectionBase):
+        if not isinstance(other, RichCollectionBase):

             return False
         if len(self._items) != len(other):
             return False
             return False
         if len(self._items) != len(other):
             return False


@@ -952,11 +1068,15 @@ class SynchronizedCollectionBase(CollectionBase):
         return not self.__eq__(other)
 
 
         return not self.__eq__(other)
 
 

-class Collection(SynchronizedCollectionBase):
-    """Represents the root of an Arvados Collection, which may be associated with
-    an API server Collection record.
+class Collection(RichCollectionBase):
+    """Represents the root of an Arvados Collection.

 
 

-    Brief summary of useful methods:
+    This class is threadsafe.  The root collection object, all subcollections
+    and files are protected by a single lock (i.e. each access locks the entire
+    collection).
+
+    Brief summary of
+    useful methods:

 
     :To read an existing file:
       `c.open("myfile", "r")`
 
     :To read an existing file:
       `c.open("myfile", "r")`


@@ -982,9 +1102,8 @@ class Collection(SynchronizedCollectionBase):
     :To merge remote changes into this object:
       `c.update()`
 
     :To merge remote changes into this object:
       `c.update()`
 

-    This class is threadsafe.  The root collection object, all subcollections
-    and files are protected by a single lock (i.e. each access locks the entire
-    collection).
+    Must be associated with an API server Collection record (during
+    initialization, or using `save_new`) to use `save` or `update`

 
     """
 
 
     """
 


@@ -1031,9 +1150,7 @@ class Collection(SynchronizedCollectionBase):
         self._manifest_text = None
         self._api_response = None
 
         self._manifest_text = None
         self._api_response = None
 

-        self._sync = SYNC_EXPLICIT

         self.lock = threading.RLock()
         self.lock = threading.RLock()

-        self.callbacks = []

         self.events = None
 
         if manifest_locator_or_text:
         self.events = None
 
         if manifest_locator_or_text:


@@ -1047,8 +1164,10 @@ class Collection(SynchronizedCollectionBase):
                 raise errors.ArgumentError(
                     "Argument to CollectionReader must be a manifest or a collection UUID")
 
                 raise errors.ArgumentError(
                     "Argument to CollectionReader must be a manifest or a collection UUID")
 

-            self._populate()
-
+            try:
+                self._populate()
+            except (IOError, errors.SyntaxError) as e:
+                raise errors.ArgumentError("Error processing manifest text: %s", e)

 
     def root_collection(self):
         return self
 
     def root_collection(self):
         return self


@@ -1056,16 +1175,14 @@ class Collection(SynchronizedCollectionBase):
     def stream_name(self):
         return "."
 
     def stream_name(self):
         return "."
 

-    def sync_mode(self):
-        return self._sync
+    def writable(self):
+        return True

 
     @synchronized
     @retry_method
     def update(self, other=None, num_retries=None):
 
     @synchronized
     @retry_method
     def update(self, other=None, num_retries=None):

-        """Fetch the latest collection record on the API server and merge it with the
-        current collection contents.
+        """Merge the latest collection on the API server with the current collection."""

 
 

-        """

         if other is None:
             if self._manifest_locator is None:
                 raise errors.ArgumentError("`other` is None but collection does not have a manifest_locator uuid")
         if other is None:
             if self._manifest_locator is None:
                 raise errors.ArgumentError("`other` is None but collection does not have a manifest_locator uuid")


@@ -1146,7 +1263,7 @@ class Collection(SynchronizedCollectionBase):
             error_via_keep = self._populate_from_keep()
         if self._manifest_text is None:
             # Nothing worked!
             error_via_keep = self._populate_from_keep()
         if self._manifest_text is None:
             # Nothing worked!

-            raise arvados.errors.NotFoundError(
+            raise errors.NotFoundError(

                 ("Failed to retrieve collection '{}' " +
                  "from either API server ({}) or Keep ({})."
                  ).format(
                 ("Failed to retrieve collection '{}' " +
                  "from either API server ({}) or Keep ({})."
                  ).format(


@@ -1166,13 +1283,28 @@ class Collection(SynchronizedCollectionBase):
 
     def __exit__(self, exc_type, exc_value, traceback):
         """Support scoped auto-commit in a with: block."""
 
     def __exit__(self, exc_type, exc_value, traceback):
         """Support scoped auto-commit in a with: block."""

-        if self._sync != SYNC_READONLY and self._has_collection_uuid():
-            self.save()
+        if exc_type is None:
+            if self.writable() and self._has_collection_uuid():
+                self.save()

         if self._block_manager is not None:
             self._block_manager.stop_threads()
 
     @synchronized
         if self._block_manager is not None:
             self._block_manager.stop_threads()
 
     @synchronized

-    def clone(self, new_parent=None, readonly=False, new_config=None):
+    def manifest_locator(self):
+        """Get the manifest locator, if any.
+
+        The manifest locator will be set when the collection is loaded from an
+        API server record or the portable data hash of a manifest.
+
+        The manifest locator will be None if the collection is newly created or
+        was created directly from manifest text.  The method `save_new()` will
+        assign a manifest locator.
+
+        """
+        return self._manifest_locator
+
+    @synchronized
+    def clone(self, new_parent=None, new_name=None, readonly=False, new_config=None):

         if new_config is None:
             new_config = self._config
         if readonly:
         if new_config is None:
             new_config = self._config
         if readonly:


@@ -1180,9 +1312,7 @@ class Collection(SynchronizedCollectionBase):
         else:
             newcollection = Collection(parent=new_parent, apiconfig=new_config)
 
         else:
             newcollection = Collection(parent=new_parent, apiconfig=new_config)
 

-        newcollection._sync = None
-        self._cloneinto(newcollection)
-        newcollection._sync = SYNC_READONLY if readonly else SYNC_EXPLICIT
+        newcollection._clonefrom(self)

         return newcollection
 
     @synchronized
         return newcollection
 
     @synchronized


@@ -1196,21 +1326,21 @@ class Collection(SynchronizedCollectionBase):
         return self._api_response
 
     def find_or_create(self, path, create_type):
         return self._api_response
 
     def find_or_create(self, path, create_type):

-        """See `SynchronizedCollectionBase.find_or_create`"""
+        """See `RichCollectionBase.find_or_create`"""

         if path == ".":
             return self
         else:
             return super(Collection, self).find_or_create(path[2:] if path.startswith("./") else path, create_type)
 
     def find(self, path):
         if path == ".":
             return self
         else:
             return super(Collection, self).find_or_create(path[2:] if path.startswith("./") else path, create_type)
 
     def find(self, path):

-        """See `SynchronizedCollectionBase.find`"""
+        """See `RichCollectionBase.find`"""

         if path == ".":
             return self
         else:
             return super(Collection, self).find(path[2:] if path.startswith("./") else path)
 
     def remove(self, path, recursive=False):
         if path == ".":
             return self
         else:
             return super(Collection, self).find(path[2:] if path.startswith("./") else path)
 
     def remove(self, path, recursive=False):

-        """See `SynchronizedCollectionBase.remove`"""
+        """See `RichCollectionBase.remove`"""

         if path == ".":
             raise errors.ArgumentError("Cannot remove '.'")
         else:
         if path == ".":
             raise errors.ArgumentError("Cannot remove '.'")
         else:


@@ -1220,26 +1350,32 @@ class Collection(SynchronizedCollectionBase):
     @synchronized
     @retry_method
     def save(self, merge=True, num_retries=None):
     @synchronized
     @retry_method
     def save(self, merge=True, num_retries=None):

-        """Commit pending buffer blocks to Keep, merge with remote record (if
-        update=True), write the manifest to Keep, and update the collection
-        record.
+        """Save collection to an existing collection record.
+
+        Commit pending buffer blocks to Keep, merge with remote record (if
+        merge=True, the default), and update the collection record.  Returns
+        the current manifest text.

 
         Will raise AssertionError if not associated with a collection record on
         the API server.  If you want to save a manifest to Keep only, see
         `save_new()`.
 
 
         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()`.
 

-        :update:
+        :merge:

           Update and merge remote changes before saving.  Otherwise, any
           remote changes will be ignored and overwritten.
 
           Update and merge remote changes before saving.  Otherwise, any
           remote changes will be ignored and overwritten.
 

+        :num_retries:
+          Retry count on API calls (if None,  use the collection default)
+

         """
         if self.modified():
             if not self._has_collection_uuid():
                 raise AssertionError("Collection manifest_locator must be a collection uuid.  Use save_new() for new collections.")
         """
         if self.modified():
             if not self._has_collection_uuid():
                 raise AssertionError("Collection manifest_locator must be a collection uuid.  Use save_new() for new collections.")

+

             self._my_block_manager().commit_all()
             self._my_block_manager().commit_all()

+

             if merge:
                 self.update()
             if merge:
                 self.update()

-            self._my_keep().put(self.manifest_text(strip=True), num_retries=num_retries)

 
             text = self.manifest_text(strip=False)
             self._api_response = self._my_api().collections().update(
 
             text = self.manifest_text(strip=False)
             self._api_response = self._my_api().collections().update(


@@ -1250,22 +1386,30 @@ class Collection(SynchronizedCollectionBase):
             self._manifest_text = self._api_response["manifest_text"]
             self.set_unmodified()
 
             self._manifest_text = self._api_response["manifest_text"]
             self.set_unmodified()
 

+        return self._manifest_text
+

 
     @must_be_writable
     @synchronized
     @retry_method
 
     @must_be_writable
     @synchronized
     @retry_method

-    def save_new(self, name=None, create_collection_record=True, owner_uuid=None, ensure_unique_name=False, num_retries=None):
-        """Commit pending buffer blocks to Keep, write the manifest to Keep, and create
-        a new collection record (if create_collection_record True).
-
-        After creating a new collection record, this Collection object will be
-        associated with the new record used by `save()`.
+    def save_new(self, name=None,
+                 create_collection_record=True,
+                 owner_uuid=None,
+                 ensure_unique_name=False,
+                 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
+        the new record used by `save()`.  Returns the current manifest text.

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

-        :keep_only:
-          Only save the manifest to keep, do not create a collection record.
+        :create_collection_record:
+           If True, create a collection record on the API server.
+           If False, only commit blocks to Keep and return the manifest text.

 
         :owner_uuid:
           the user, or project uuid that will own this collection.
 
         :owner_uuid:
           the user, or project uuid that will own this collection.


@@ -1276,14 +1420,17 @@ class Collection(SynchronizedCollectionBase):
           if it conflicts with a collection with the same name and owner.  If
           False, a name conflict will result in an error.
 
           if it conflicts with a collection with the same name and owner.  If
           False, a name conflict will result in an error.
 

+        :num_retries:
+          Retry count on API calls (if None,  use the collection default)
+

         """
         self._my_block_manager().commit_all()
         """
         self._my_block_manager().commit_all()

-        self._my_keep().put(self.manifest_text(strip=True), num_retries=num_retries)

         text = self.manifest_text(strip=False)
 
         if create_collection_record:
             if name is None:
                 name = "Collection created %s" % (time.strftime("%Y-%m-%d %H:%M:%S %Z", time.localtime()))
         text = self.manifest_text(strip=False)
 
         if create_collection_record:
             if name is None:
                 name = "Collection created %s" % (time.strftime("%Y-%m-%d %H:%M:%S %Z", time.localtime()))

+                ensure_unique_name = True

 
             body = {"manifest_text": text,
                     "name": name}
 
             body = {"manifest_text": text,
                     "name": name}


@@ -1295,21 +1442,10 @@ class Collection(SynchronizedCollectionBase):
 
             self._manifest_locator = self._api_response["uuid"]
 
 
             self._manifest_locator = self._api_response["uuid"]
 

-        self._manifest_text = text
-        self.set_unmodified()
-
-    @synchronized
-    def subscribe(self, callback):
-        self.callbacks.append(callback)
+            self._manifest_text = text
+            self.set_unmodified()

 
 

-    @synchronized
-    def unsubscribe(self, callback):
-        self.callbacks.remove(callback)
-
-    @synchronized
-    def notify(self, event, collection, name, item):
-        for c in self.callbacks:
-            c(event, collection, name, item)
+        return text

 
     @synchronized
     def _import_manifest(self, manifest_text):
 
     @synchronized
     def _import_manifest(self, manifest_text):


@@ -1322,9 +1458,6 @@ class Collection(SynchronizedCollectionBase):
         if len(self) > 0:
             raise ArgumentError("Can only import manifest into an empty collection")
 
         if len(self) > 0:
             raise ArgumentError("Can only import manifest into an empty collection")
 

-        save_sync = self.sync_mode()
-        self._sync = None
-

         STREAM_NAME = 0
         BLOCKS = 1
         SEGMENTS = 2
         STREAM_NAME = 0
         BLOCKS = 1
         SEGMENTS = 2


@@ -1332,9 +1465,9 @@ class Collection(SynchronizedCollectionBase):
         stream_name = None
         state = STREAM_NAME
 
         stream_name = None
         state = STREAM_NAME
 

-        for n in re.finditer(r'(\S+)(\s+|$)', manifest_text):
-            tok = n.group(1)
-            sep = n.group(2)
+        for token_and_separator in re.finditer(r'(\S+)(\s+|$)', manifest_text):
+            tok = token_and_separator.group(1)
+            sep = token_and_separator.group(2)

 
             if state == STREAM_NAME:
                 # starting a new stream
 
             if state == STREAM_NAME:
                 # starting a new stream


@@ -1343,27 +1476,28 @@ class Collection(SynchronizedCollectionBase):
                 segments = []
                 streamoffset = 0L
                 state = BLOCKS
                 segments = []
                 streamoffset = 0L
                 state = BLOCKS

+                self.mkdirs(stream_name)

                 continue
 
             if state == BLOCKS:
                 continue
 
             if state == BLOCKS:

-                s = re.match(r'[0-9a-f]{32}\+(\d+)(\+\S+)*', tok)
-                if s:
-                    blocksize = long(s.group(1))
-                    blocks.append(Range(tok, streamoffset, blocksize))
+                block_locator = re.match(r'[0-9a-f]{32}\+(\d+)(\+\S+)*', tok)
+                if block_locator:
+                    blocksize = long(block_locator.group(1))
+                    blocks.append(Range(tok, streamoffset, blocksize, 0))

                     streamoffset += blocksize
                 else:
                     state = SEGMENTS
 
             if state == SEGMENTS:
                     streamoffset += blocksize
                 else:
                     state = SEGMENTS
 
             if state == SEGMENTS:

-                s = re.search(r'^(\d+):(\d+):(\S+)', tok)
-                if s:
-                    pos = long(s.group(1))
-                    size = long(s.group(2))
-                    name = s.group(3).replace('\\040', ' ')
+                file_segment = re.search(r'^(\d+):(\d+):(\S+)', tok)
+                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)
                     filepath = os.path.join(stream_name, name)

-                    f = self.find_or_create(filepath, FILE)
-                    if isinstance(f, ArvadosFile):
-                        f.add_segment(blocks, pos, size)
+                    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:
                     else:
                         raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath)
                 else:


@@ -1375,10 +1509,14 @@ class Collection(SynchronizedCollectionBase):
                 state = STREAM_NAME
 
         self.set_unmodified()
                 state = STREAM_NAME
 
         self.set_unmodified()

-        self._sync = save_sync
+
+    @synchronized
+    def notify(self, event, collection, name, item):
+        if self._callback:
+            self._callback(event, collection, name, item)

 
 
 
 

-class Subcollection(SynchronizedCollectionBase):
+class Subcollection(RichCollectionBase):

     """This is a subdirectory within a collection that doesn't have its own API
     server record.
 
     """This is a subdirectory within a collection that doesn't have its own API
     server record.
 


@@ -1386,16 +1524,18 @@ class Subcollection(SynchronizedCollectionBase):
 
     """
 
 
     """
 

-    def __init__(self, parent):
+    def __init__(self, parent, name):

         super(Subcollection, self).__init__(parent)
         self.lock = self.root_collection().lock
         self._manifest_text = None
         super(Subcollection, self).__init__(parent)
         self.lock = self.root_collection().lock
         self._manifest_text = None

+        self.name = name
+        self.num_retries = parent.num_retries

 
     def root_collection(self):
         return self.parent.root_collection()
 
 
     def root_collection(self):
         return self.parent.root_collection()
 

-    def sync_mode(self):
-        return self.root_collection().sync_mode()
+    def writable(self):
+        return self.root_collection().writable()

 
     def _my_api(self):
         return self.root_collection()._my_api()
 
     def _my_api(self):
         return self.root_collection()._my_api()


@@ -1406,43 +1546,39 @@ class Subcollection(SynchronizedCollectionBase):
     def _my_block_manager(self):
         return self.root_collection()._my_block_manager()
 
     def _my_block_manager(self):
         return self.root_collection()._my_block_manager()
 

-    def notify(self, event, collection, name, item):
-        return self.root_collection().notify(event, collection, name, item)
-

     def stream_name(self):
     def stream_name(self):

-        for k, v in self.parent.items():
-            if v is self:
-                return os.path.join(self.parent.stream_name(), k)
-        return '.'
+        return os.path.join(self.parent.stream_name(), self.name)

 
     @synchronized
 
     @synchronized

-    def clone(self, new_parent):
-        c = Subcollection(new_parent)
-        self._cloneinto(c)
+    def clone(self, new_parent, new_name):
+        c = Subcollection(new_parent, new_name)
+        c._clonefrom(self)

         return c
 
 
 class CollectionReader(Collection):
         return c
 
 
 class CollectionReader(Collection):

-    """A read-only collection object from an api collection record locator,
-    a portable data hash of a manifest, or raw manifest text.
+    """A read-only collection object.

 
 

-    See `Collection` constructor for detailed options.
+    Initialize from an api collection record locator, a portable data hash of a
+    manifest, or raw manifest text.  See `Collection` constructor for detailed
+    options.

 
     """
 
     """

-    def __init__(self, *args, **kwargs):
-        if not args and not kwargs.get("manifest_locator_or_text"):
-            raise errors.ArgumentError("Must provide manifest locator or text to initialize ReadOnlyCollection")
-
-        super(CollectionReader, self).__init__(*args, **kwargs)
+    def __init__(self, manifest_locator_or_text, *args, **kwargs):
+        self._in_init = True
+        super(CollectionReader, self).__init__(manifest_locator_or_text, *args, **kwargs)
+        self._in_init = False

 
         # Forego any locking since it should never change once initialized.
         self.lock = NoopLock()
 
         # Forego any locking since it should never change once initialized.
         self.lock = NoopLock()

-        self._sync = SYNC_READONLY

 
         # Backwards compatability with old CollectionReader
         # all_streams() and all_files()
         self._streams = None
 
 
         # Backwards compatability with old CollectionReader
         # all_streams() and all_files()
         self._streams = None
 

+    def writable(self):
+        return self._in_init
+

     def _populate_streams(orig_func):
         @functools.wraps(orig_func)
         def populate_streams_wrapper(self, *args, **kwargs):
     def _populate_streams(orig_func):
         @functools.wraps(orig_func)
         def populate_streams_wrapper(self, *args, **kwargs):