5990: If --docker-image not specified, don't provide

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

diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py
index 12fa9ae30d5bcd7bb4a539cc947bca881ab59302..38e794c24a217ffa5c76c1a7b026e4d432d369a0 100644 (file)
--- a/sdk/python/arvados/collection.py
+++ b/sdk/python/arvados/collection.py
@@ -470,13 +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


@@ -486,7 +487,8 @@ class SynchronizedCollectionBase(CollectionBase):
 
     def __init__(self, parent=None):
         self.parent = parent
 
     def __init__(self, parent=None):
         self.parent = parent

-        self._modified = True
+        self._committed = False
+        self._callback = None

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


@@ -536,24 +538,24 @@ class SynchronizedCollectionBase(CollectionBase):
                 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._items[pathcomponents[0]] = item

-                    self._modified = True
+                    self._committed = False

                     self.notify(ADD, self, pathcomponents[0], item)
                 return item
             else:
                 if item is None:
                     # create new collection
                     self.notify(ADD, self, pathcomponents[0], item)
                 return item
             else:
                 if item is None:
                     # create new collection

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

                     self._items[pathcomponents[0]] = item
                     self._items[pathcomponents[0]] = item

-                    self._modified = True
+                    self._committed = False

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

-                if isinstance(item, SynchronizedCollectionBase):
+                if isinstance(item, RichCollectionBase):

                     return item.find_or_create(pathcomponents[1], create_type)
                 else:
                     return item.find_or_create(pathcomponents[1], create_type)
                 else:

-                    raise IOError((errno.ENOTDIR, "Interior path components must be subcollection"))
+                    raise IOError(errno.ENOTDIR, "Not a directory: '%s'" % pathcomponents[0])

         else:
             return self
 
         else:
             return self
 


@@ -566,28 +568,33 @@ class SynchronizedCollectionBase(CollectionBase):
 
         """
         if not path:
 
         """
         if not path:

-            raise errors.ArgumentError("Parameter 'path' must not be empty.")
+            raise errors.ArgumentError("Parameter 'path' is empty.")

 
         pathcomponents = path.split("/", 1)
         item = self._items.get(pathcomponents[0])
         if len(pathcomponents) == 1:
             return item
         else:
 
         pathcomponents = path.split("/", 1)
         item = self._items.get(pathcomponents[0])
         if len(pathcomponents) == 1:
             return item
         else:

-            if isinstance(item, SynchronizedCollectionBase):
+            if isinstance(item, RichCollectionBase):

                 if pathcomponents[1]:
                     return item.find(pathcomponents[1])
                 else:
                     return item
             else:
                 if pathcomponents[1]:
                     return item.find(pathcomponents[1])
                 else:
                     return item
             else:

-                raise IOError((errno.ENOTDIR, "Interior path components must be subcollection"))
+                raise IOError(errno.ENOTDIR, "Is not a directory: %s" % pathcomponents[0])

 
 

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

         """Recursive subcollection create.
 
         """Recursive subcollection create.
 

-        Like `os.mkdirs()`.  Will create intermediate subcollections needed to
-        contain the leaf subcollection path.
+        Like `os.makedirs()`.  Will create intermediate subcollections needed
+        to contain the leaf subcollection path.

 
         """
 
         """

+
+        if self.find(path) != None:
+            raise IOError(errno.EEXIST, "Directory or file exists: '%s'" % path)
+

         return self.find_or_create(path, COLLECTION)
 
     def open(self, path, mode="r"):
         return self.find_or_create(path, COLLECTION)
 
     def open(self, path, mode="r"):


@@ -614,7 +621,7 @@ class SynchronizedCollectionBase(CollectionBase):
         create = (mode != "r")
 
         if create and not self.writable():
         create = (mode != "r")
 
         if create and not self.writable():

-            raise IOError((errno.EROFS, "Collection is read only"))
+            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)


@@ -622,9 +629,9 @@ 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, "Is a directory: %s" % path)

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


@@ -632,26 +639,31 @@ 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, 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):
     def modified(self):

-        """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 v.modified():
-                return True
-        return False
+        """Determine if the collection has been modified since last commited."""
+        return not self.committed()
+
+    @synchronized
+    def committed(self):
+        """Determine if the collection has been committed to the API server."""
+
+        if self._committed is False:
+            return False
+        for v in self._items.values():
+            if v.committed() is False:
+                return False
+        return True

 
     @synchronized
 
     @synchronized

-    def set_unmodified(self):
-        """Recursively clear modified flag."""
-        self._modified = False
+    def set_committed(self):
+        """Recursively set committed flag to True."""
+        self._committed = True

         for k,v in self._items.items():
         for k,v in self._items.items():

-            v.set_unmodified()
+            v.set_committed()

 
     @synchronized
     def __iter__(self):
 
     @synchronized
     def __iter__(self):


@@ -682,7 +694,7 @@ class SynchronizedCollectionBase(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._modified = True
+        self._committed = False

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


@@ -702,7 +714,7 @@ 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


@@ -714,57 +726,82 @@ class SynchronizedCollectionBase(CollectionBase):
         """
 
         if not path:
         """
 
         if not path:

-            raise errors.ArgumentError("Parameter 'path' must not be empty.")
+            raise errors.ArgumentError("Parameter 'path' is empty.")

 
         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")

         if len(pathcomponents) == 1:
         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"))
+            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]]
             deleteditem = self._items[pathcomponents[0]]
             del self._items[pathcomponents[0]]

-            self._modified = True
+            self._committed = False

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

-            self._items[k] = v.clone(self)
+            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._committed = False
+
+        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


@@ -774,40 +811,99 @@ 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
+    def rename(self, source, target_path, source_collection=None, overwrite=False):
+        """Move a file or subcollection from `source_collection` to a new path in this collection.
+
+        :source:
+          A string with a path to source file or subcollection.
+
+        :target_path:
+          Destination file or path.  If the target path already exists and is a
+          subcollection, the item will be placed inside the subcollection.  If
+          the target path already exists and is a file, this will raise an error
+          unless you specify `overwrite=True`.
+
+        :source_collection:
+          Collection to copy `source_path` from (default `self`)
+
+        :overwrite:
+          Whether to overwrite target file if it already exists.
+        """
+
+        source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, False)
+        if not source_obj.writable():
+            raise IOError(errno.EROFS, "Source collection is read only.")
+        target_dir.add(source_obj, target_name, overwrite, True)
+
+    def portable_manifest_text(self, stream_name="."):
+        """Get the manifest text for this collection, sub collections and files.
+
+        This method does not flush outstanding blocks to Keep.  It will return
+        a normalized manifest with access tokens stripped.
+
+        :stream_name:
+          Name to use for this stream (directory)
+
+        """
+        return self._get_manifest_text(stream_name, True, True)

 
     @synchronized
     def manifest_text(self, stream_name=".", strip=False, normalize=False):
         """Get the manifest text for this collection, sub collections and files.
 
 
     @synchronized
     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.
 
         :strip:
           If True, remove signing tokens from block locators if present.


@@ -821,14 +917,35 @@ class SynchronizedCollectionBase(CollectionBase):
 
         """
 
 
         """
 

-        if self.modified() or self._manifest_text is None or normalize:
-            item  = self
+        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.
+          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.
+
+        """
+
+        if not self.committed() or self._manifest_text is None or normalize:

             stream = {}
             buf = []
             stream = {}
             buf = []

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


@@ -841,8 +958,8 @@ class SynchronizedCollectionBase(CollectionBase):
                 stream[filename] = filestream
             if stream:
                 buf.append(" ".join(normalize_stream(stream_name, stream)) + "\n")
                 stream[filename] = filestream
             if stream:
                 buf.append(" ".join(normalize_stream(stream_name, stream)) + "\n")

-            for dirname in [s for s in sorted_keys if isinstance(item[s], SynchronizedCollectionBase)]:
-                buf.append(item[dirname].manifest_text(stream_name=os.path.join(stream_name, dirname), strip=strip))
+            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 "".join(buf)
         else:
             if strip:


@@ -862,15 +979,15 @@ class SynchronizedCollectionBase(CollectionBase):
             holding_collection = Collection(api_client=self._my_api(), keep_client=self._my_keep())
         for k in self:
             if k not in end_collection:
             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


@@ -882,12 +999,14 @@ class SynchronizedCollectionBase(CollectionBase):
         alternate path indicating the conflict.
 
         """
         alternate path indicating the conflict.
 
         """

+        if changes:
+            self._committed = False

         for change in changes:
             event_type = change[0]
             path = change[1]
             initial = change[2]
             local = self.find(path)
         for change in changes:
             event_type = change[0]
             path = change[1]
             initial = change[2]
             local = self.find(path)

-            conflictpath = "%s~conflict-%s~" % (path, time.strftime("%Y-%m-%d-%H:%M:%S",
+            conflictpath = "%s~%s~conflict~" % (path, time.strftime("%Y%m%d-%H%M%S",

                                                                     time.gmtime()))
             if event_type == ADD:
                 if local is None:
                                                                     time.gmtime()))
             if event_type == ADD:
                 if local is None:


@@ -922,14 +1041,32 @@ 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


@@ -943,8 +1080,14 @@ class SynchronizedCollectionBase(CollectionBase):
     def __ne__(self, other):
         return not self.__eq__(other)
 
     def __ne__(self, other):
         return not self.__eq__(other)
 

+    @synchronized
+    def flush(self):
+        """Flush bufferblocks to Keep."""
+        for e in self.values():
+            e.flush()
+

 
 

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

     """Represents the root of an Arvados Collection.
 
     This class is threadsafe.  The root collection object, all subcollections
     """Represents the root of an Arvados Collection.
 
     This class is threadsafe.  The root collection object, all subcollections


@@ -1025,9 +1168,9 @@ class Collection(SynchronizedCollectionBase):
         self._manifest_locator = None
         self._manifest_text = None
         self._api_response = None
         self._manifest_locator = None
         self._manifest_text = None
         self._api_response = None

+        self._past_versions = set()

 
         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:


@@ -1039,7 +1182,7 @@ class Collection(SynchronizedCollectionBase):
                 self._manifest_text = manifest_locator_or_text
             else:
                 raise errors.ArgumentError(
                 self._manifest_text = manifest_locator_or_text
             else:
                 raise errors.ArgumentError(

-                    "Argument to CollectionReader must be a manifest or a collection UUID")
+                    "Argument to CollectionReader is not a manifest or a collection UUID")

 
             try:
                 self._populate()
 
             try:
                 self._populate()


@@ -1055,6 +1198,10 @@ class Collection(SynchronizedCollectionBase):
     def writable(self):
         return True
 
     def writable(self):
         return True
 

+    @synchronized
+    def known_past_version(self, modified_at_and_portable_data_hash):
+        return modified_at_and_portable_data_hash in self._past_versions
+

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


@@ -1064,9 +1211,15 @@ class Collection(SynchronizedCollectionBase):
             if self._manifest_locator is None:
                 raise errors.ArgumentError("`other` is None but collection does not have a manifest_locator uuid")
             response = self._my_api().collections().get(uuid=self._manifest_locator).execute(num_retries=num_retries)
             if self._manifest_locator is None:
                 raise errors.ArgumentError("`other` is None but collection does not have a manifest_locator uuid")
             response = self._my_api().collections().get(uuid=self._manifest_locator).execute(num_retries=num_retries)

+            if self.known_past_version((response.get("modified_at"), response.get("portable_data_hash"))):
+                # We've merged this record this before.  Don't do anything.
+                return
+            else:
+                self._past_versions.add((response.get("modified_at"), response.get("portable_data_hash")))

             other = CollectionReader(response["manifest_text"])
         baseline = CollectionReader(self._manifest_text)
         self.apply(baseline.diff(other))
             other = CollectionReader(response["manifest_text"])
         baseline = CollectionReader(self._manifest_text)
         self.apply(baseline.diff(other))

+        self._manifest_text = self.manifest_text()

 
     @synchronized
     def _my_api(self):
 
     @synchronized
     def _my_api(self):


@@ -1090,6 +1243,10 @@ class Collection(SynchronizedCollectionBase):
             self._block_manager = _BlockManager(self._my_keep())
         return self._block_manager
 
             self._block_manager = _BlockManager(self._my_keep())
         return self._block_manager
 

+    def _remember_api_response(self, response):
+        self._api_response = response
+        self._past_versions.add((response.get("modified_at"), response.get("portable_data_hash")))
+

     def _populate_from_api_server(self):
         # As in KeepClient itself, we must wait until the last
         # possible moment to instantiate an API client, in order to
     def _populate_from_api_server(self):
         # As in KeepClient itself, we must wait until the last
         # possible moment to instantiate an API client, in order to


@@ -1099,9 +1256,9 @@ class Collection(SynchronizedCollectionBase):
         # clause, just like any other Collection lookup
         # failure. Return an exception, or None if successful.
         try:
         # clause, just like any other Collection lookup
         # failure. Return an exception, or None if successful.
         try:

-            self._api_response = self._my_api().collections().get(
+            self._remember_api_response(self._my_api().collections().get(

                 uuid=self._manifest_locator).execute(
                 uuid=self._manifest_locator).execute(

-                    num_retries=self.num_retries)
+                    num_retries=self.num_retries))

             self._manifest_text = self._api_response['manifest_text']
             return None
         except Exception as e:
             self._manifest_text = self._api_response['manifest_text']
             return None
         except Exception as e:


@@ -1160,14 +1317,31 @@ 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 exc_type is not None:
+        if exc_type is None:

             if self.writable() and self._has_collection_uuid():
                 self.save()
             if self.writable() and self._has_collection_uuid():
                 self.save()

+        self.stop_threads()
+
+    def stop_threads(self):

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


@@ -1189,21 +1363,21 @@ 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:


@@ -1216,52 +1390,63 @@ class Collection(SynchronizedCollectionBase):
         """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

-        update=True), write the manifest to Keep, and update the collection
-        record.
+        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.committed():

             if not self._has_collection_uuid():
             if not self._has_collection_uuid():

-                raise AssertionError("Collection manifest_locator must be a collection uuid.  Use save_new() for new collections.")
+                raise AssertionError("Collection manifest_locator is not 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)
 
             text = self.manifest_text(strip=False)

-            self._api_response = self._my_api().collections().update(
+            self._remember_api_response(self._my_api().collections().update(

                 uuid=self._manifest_locator,
                 body={'manifest_text': text}
                 ).execute(
                 uuid=self._manifest_locator,
                 body={'manifest_text': text}
                 ).execute(

-                    num_retries=num_retries)
+                    num_retries=num_retries))

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

-            self.set_unmodified()
+            self.set_committed()
+
+        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):
+    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.
 
         """Save collection to a new collection record.
 

-        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()`.
+        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.


@@ -1272,40 +1457,32 @@ 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:
         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()))
+                name = "New collection"
+                ensure_unique_name = True

 
             body = {"manifest_text": text,
                     "name": name}
             if owner_uuid:
                 body["owner_uuid"] = owner_uuid
 
 
             body = {"manifest_text": text,
                     "name": name}
             if owner_uuid:
                 body["owner_uuid"] = owner_uuid
 

-            self._api_response = self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries)
+            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"]
 
             text = self._api_response["manifest_text"]
 
             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_committed()

 
 

-    @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):


@@ -1336,13 +1513,14 @@ class Collection(SynchronizedCollectionBase):
                 segments = []
                 streamoffset = 0L
                 state = BLOCKS
                 segments = []
                 streamoffset = 0L
                 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)
                 if block_locator:
                     blocksize = long(block_locator.group(1))
                 continue
 
             if state == BLOCKS:
                 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))
+                    blocks.append(Range(tok, streamoffset, blocksize, 0))

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


@@ -1361,27 +1539,34 @@ class Collection(SynchronizedCollectionBase):
                         raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath)
                 else:
                     # error!
                         raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath)
                 else:
                     # error!

-                    raise errors.SyntaxError("Invalid manifest format")
+                    raise errors.SyntaxError("Invalid manifest format, expected file segment but did not match format: '%s'" % tok)

 
             if sep == "\n":
                 stream_name = None
                 state = STREAM_NAME
 
 
             if sep == "\n":
                 stream_name = None
                 state = STREAM_NAME
 

-        self.set_unmodified()
+        self.set_committed()

 
 

+    @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.
 

-    It falls under the umbrella of the root collection.
+    Subcollection locking falls under the umbrella lock of its root collection.

 
     """
 
 
     """
 

-    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()


@@ -1398,21 +1583,25 @@ 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)
+    def clone(self, new_parent, new_name):
+        c = Subcollection(new_parent, new_name)

         c._clonefrom(self)
         return c
 
         c._clonefrom(self)
         return c
 

+    @must_be_writable
+    @synchronized
+    def _reparent(self, newparent, newname):
+        self._committed = False
+        self.flush()
+        self.parent.remove(self.name, recursive=True)
+        self.parent = newparent
+        self.name = newname
+        self.lock = self.parent.root_collection().lock
+

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