Added --storage-classes argument to arv-put.

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

diff --git a/sdk/python/arvados/collection.py b/sdk/python/arvados/collection.py
index 812438e2ccf493507d06ca9468e3c9418f9e0e69..cce7d75685628525e17775b9b6767b0017d5d969 100644 (file)
--- a/sdk/python/arvados/collection.py
+++ b/sdk/python/arvados/collection.py
@@ -1,3 +1,12 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+from __future__ import absolute_import
+from future.utils import listitems, listvalues, viewkeys
+from builtins import str
+from past.builtins import basestring
+from builtins import object

 import functools
 import logging
 import os
 import functools
 import logging
 import os


@@ -11,20 +20,22 @@ from collections import deque
 from stat import *
 
 from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, _BlockManager, synchronized, must_be_writable, NoopLock
 from stat import *
 
 from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, _BlockManager, synchronized, must_be_writable, NoopLock

-from keep import KeepLocator, KeepClient
+from .keep import KeepLocator, KeepClient

 from .stream import StreamReader
 from ._normalize_stream import normalize_stream
 from ._ranges import Range, LocatorAndRange
 from .safeapi import ThreadSafeApiCache
 from .stream import StreamReader
 from ._normalize_stream import normalize_stream
 from ._ranges import Range, LocatorAndRange
 from .safeapi import ThreadSafeApiCache

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

 from arvados.retry import retry_method
 
 _logger = logging.getLogger('arvados.collection')
 
 class CollectionBase(object):
 from arvados.retry import retry_method
 
 _logger = logging.getLogger('arvados.collection')
 
 class CollectionBase(object):

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

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


@@ -51,7 +62,7 @@ class CollectionBase(object):
             if fields:
                 clean_fields = fields[:1] + [
                     (re.sub(r'\+[^\d][^\+]*', '', x)
             if fields:
                 clean_fields = fields[:1] + [
                     (re.sub(r'\+[^\d][^\+]*', '', x)

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

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


@@ -82,6 +93,8 @@ class _WriterFile(_FileLikeObjectBase):
 
 
 class CollectionWriter(CollectionBase):
 
 
 class CollectionWriter(CollectionBase):

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

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


@@ -180,7 +193,7 @@ class CollectionWriter(CollectionBase):
 
     def _work_trees(self):
         path, stream_name, max_manifest_depth = self._queued_trees[0]
 
     def _work_trees(self):
         path, stream_name, max_manifest_depth = self._queued_trees[0]

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

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


@@ -216,7 +229,11 @@ class CollectionWriter(CollectionBase):
         self.do_queued_work()
 
     def write(self, newdata):
         self.do_queued_work()
 
     def write(self, newdata):

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

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


@@ -256,7 +273,7 @@ class CollectionWriter(CollectionBase):
         return self._last_open
 
     def flush_data(self):
         return self._last_open
 
     def flush_data(self):

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

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


@@ -346,11 +363,12 @@ class CollectionWriter(CollectionBase):
         sending manifest_text() to the API server's "create
         collection" endpoint.
         """
         sending manifest_text() to the API server's "create
         collection" endpoint.
         """

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

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

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

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


@@ -372,8 +390,18 @@ class CollectionWriter(CollectionBase):
             ret += locators
         return ret
 
             ret += locators
         return ret
 

+    def save_new(self, name=None):
+        return self._api_client.collections().create(
+            ensure_unique_name=True,
+            body={
+                'name': name,
+                'manifest_text': self.manifest_text(),
+            }).execute(num_retries=self.num_retries)
+

 
 class ResumableCollectionWriter(CollectionWriter):
 
 class ResumableCollectionWriter(CollectionWriter):

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

     STATE_PROPS = ['_current_stream_files', '_current_stream_length',
                    '_current_stream_locators', '_current_stream_name',
                    '_current_file_name', '_current_file_pos', '_close_file',
     STATE_PROPS = ['_current_stream_files', '_current_stream_length',
                    '_current_stream_locators', '_current_stream_name',
                    '_current_file_name', '_current_file_pos', '_close_file',


@@ -418,7 +446,7 @@ class ResumableCollectionWriter(CollectionWriter):
         return writer
 
     def check_dependencies(self):
         return writer
 
     def check_dependencies(self):

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

             if not S_ISREG(orig_stat[ST_MODE]):
                 raise errors.StaleWriterStateError("{} not file".format(path))
             try:
             if not S_ISREG(orig_stat[ST_MODE]):
                 raise errors.StaleWriterStateError("{} not file".format(path))
             try:


@@ -544,7 +572,7 @@ class RichCollectionBase(CollectionBase):
                     else:
                         item = ArvadosFile(self, pathcomponents[0])
                     self._items[pathcomponents[0]] = item
                     else:
                         item = ArvadosFile(self, pathcomponents[0])
                     self._items[pathcomponents[0]] = item

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

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


@@ -552,7 +580,7 @@ class RichCollectionBase(CollectionBase):
                     # create new collection
                     item = Subcollection(self, pathcomponents[0])
                     self._items[pathcomponents[0]] = item
                     # create new collection
                     item = Subcollection(self, pathcomponents[0])
                     self._items[pathcomponents[0]] = item

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

                     self.notify(ADD, self, pathcomponents[0], item)
                 if isinstance(item, RichCollectionBase):
                     return item.find_or_create(pathcomponents[1], create_type)
                     self.notify(ADD, self, pathcomponents[0], item)
                 if isinstance(item, RichCollectionBase):
                     return item.find_or_create(pathcomponents[1], create_type)


@@ -612,7 +640,12 @@ class RichCollectionBase(CollectionBase):
         :path:
           path to a file in the collection
         :mode:
         :path:
           path to a file in the collection
         :mode:

-          one of "r", "r+", "w", "w+", "a", "a+"
+          a string consisting of "r", "w", or "a", optionally followed
+          by "b" or "t", optionally followed by "+".
+          :"b":
+            binary mode: write() accepts bytes, read() returns bytes.
+          :"t":
+            text mode (default): write() accepts strings, read() returns strings.

           :"r":
             opens for reading
           :"r+":
           :"r":
             opens for reading
           :"r+":


@@ -624,33 +657,28 @@ class RichCollectionBase(CollectionBase):
             the end of the file.  Writing does not affect the file pointer for
             reading.
         """
             the end of the file.  Writing does not affect the file pointer for
             reading.
         """

-        mode = mode.replace("b", "")
-        if len(mode) == 0 or mode[0] not in ("r", "w", "a"):
-            raise errors.ArgumentError("Bad mode '%s'" % mode)
-        create = (mode != "r")

 
 

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

 
 

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

             arvfile = self.find(path)
             arvfile = self.find(path)

+        elif not self.writable():
+            raise IOError(errno.EROFS, "Collection is read only")
+        else:
+            fclass = ArvadosFileWriter
+            arvfile = self.find_or_create(path, FILE)

 
         if arvfile is None:
             raise IOError(errno.ENOENT, "File not found", path)
         if not isinstance(arvfile, ArvadosFile):
             raise IOError(errno.EISDIR, "Is a directory", path)
 
 
         if arvfile is None:
             raise IOError(errno.ENOENT, "File not found", path)
         if not isinstance(arvfile, ArvadosFile):
             raise IOError(errno.EISDIR, "Is a directory", path)
 

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

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

-        name = os.path.basename(path)
-
-        if mode == "r":
-            return ArvadosFileReader(arvfile, num_retries=self.num_retries)
-        else:
-            return ArvadosFileWriter(arvfile, mode, num_retries=self.num_retries)
+        return fclass(arvfile, mode=mode, num_retries=self.num_retries)

 
     def modified(self):
         """Determine if the collection has been modified since last commited."""
 
     def modified(self):
         """Determine if the collection has been modified since last commited."""


@@ -659,25 +687,31 @@ class RichCollectionBase(CollectionBase):
     @synchronized
     def committed(self):
         """Determine if the collection has been committed to the API server."""
     @synchronized
     def committed(self):
         """Determine if the collection has been committed to the API server."""

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

 
     @synchronized
 
     @synchronized

-    def set_committed(self):
-        """Recursively set committed flag to True."""
-        self._committed = True
-        for k,v in self._items.items():
-            v.set_committed()
+    def set_committed(self, value=True):
+        """Recursively set committed flag.
+
+        If value is True, set committed to be True for this and all children.
+
+        If value is False, set committed to be False for this and all parents.
+        """
+        if value == self._committed:
+            return
+        if value:
+            for k,v in listitems(self._items):
+                v.set_committed(True)
+            self._committed = True
+        else:
+            self._committed = False
+            if self.parent is not None:
+                self.parent.set_committed(False)

 
     @synchronized
     def __iter__(self):
         """Iterate over names of files and collections contained in this collection."""
 
     @synchronized
     def __iter__(self):
         """Iterate over names of files and collections contained in this collection."""

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

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


@@ -703,7 +737,7 @@ class RichCollectionBase(CollectionBase):
     def __delitem__(self, p):
         """Delete an item by name which is directly contained by this collection."""
         del self._items[p]
     def __delitem__(self, p):
         """Delete an item by name which is directly contained by this collection."""
         del self._items[p]

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

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


@@ -714,12 +748,12 @@ class RichCollectionBase(CollectionBase):
     @synchronized
     def values(self):
         """Get a list of files and collection objects directly contained in this collection."""
     @synchronized
     def values(self):
         """Get a list of files and collection objects directly contained in this collection."""

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

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

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

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


@@ -746,13 +780,13 @@ class RichCollectionBase(CollectionBase):
                 raise IOError(errno.ENOTEMPTY, "Directory not empty", path)
             deleteditem = self._items[pathcomponents[0]]
             del self._items[pathcomponents[0]]
                 raise IOError(errno.ENOTEMPTY, "Directory not empty", path)
             deleteditem = self._items[pathcomponents[0]]
             del self._items[pathcomponents[0]]

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

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

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

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


@@ -795,7 +829,7 @@ class RichCollectionBase(CollectionBase):
             item = source_obj.clone(self, target_name)
 
         self._items[target_name] = item
             item = source_obj.clone(self, target_name)
 
         self._items[target_name] = item

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

 
         if modified_from:
             self.notify(MOD, self, target_name, (modified_from, item))
 
         if modified_from:
             self.notify(MOD, self, target_name, (modified_from, item))


@@ -905,7 +939,8 @@ class RichCollectionBase(CollectionBase):
         return self._get_manifest_text(stream_name, True, True)
 
     @synchronized
         return self._get_manifest_text(stream_name, True, True)
 
     @synchronized

-    def manifest_text(self, stream_name=".", strip=False, normalize=False):
+    def manifest_text(self, stream_name=".", strip=False, normalize=False,
+                      only_committed=False):

         """Get the manifest text for this collection, sub collections and files.
 
         This method will flush outstanding blocks to Keep.  By default, it will
         """Get the manifest text for this collection, sub collections and files.
 
         This method will flush outstanding blocks to Keep.  By default, it will


@@ -924,10 +959,15 @@ class RichCollectionBase(CollectionBase):
           is not modified, return the original manifest text even if it is not
           in normalized form.
 
           is not modified, return the original manifest text even if it is not
           in normalized form.
 

+        :only_committed:
+          If True, don't commit pending blocks.
+

         """
 
         """
 

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

 
     @synchronized
     def _get_manifest_text(self, stream_name, strip, normalize, only_committed=False):
 
     @synchronized
     def _get_manifest_text(self, stream_name, strip, normalize, only_committed=False):


@@ -973,7 +1013,7 @@ class RichCollectionBase(CollectionBase):
             if stream:
                 buf.append(" ".join(normalize_stream(stream_name, stream)) + "\n")
             for dirname in [s for s in sorted_keys if isinstance(self[s], RichCollectionBase)]:
             if stream:
                 buf.append(" ".join(normalize_stream(stream_name, stream)) + "\n")
             for dirname in [s for s in sorted_keys if isinstance(self[s], RichCollectionBase)]:

-                buf.append(self[dirname].manifest_text(stream_name=os.path.join(stream_name, dirname), strip=strip, normalize=True))
+                buf.append(self[dirname].manifest_text(stream_name=os.path.join(stream_name, dirname), strip=strip, normalize=True, only_committed=only_committed))

             return "".join(buf)
         else:
             if strip:
             return "".join(buf)
         else:
             if strip:


@@ -1016,7 +1056,7 @@ class RichCollectionBase(CollectionBase):
 
         """
         if changes:
 
         """
         if changes:

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

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


@@ -1057,8 +1097,13 @@ class RichCollectionBase(CollectionBase):
 
     def portable_data_hash(self):
         """Get the portable data hash for this collection's manifest."""
 
     def portable_data_hash(self):
         """Get the portable data hash for this collection's manifest."""

-        stripped = self.portable_manifest_text()
-        return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
+        if self._manifest_locator and self.committed():
+            # If the collection is already saved on the API server, and it's committed
+            # then return API server's PDH response.
+            return self._portable_data_hash
+        else:
+            stripped = self.portable_manifest_text().encode()
+            return '{}+{}'.format(hashlib.md5(stripped).hexdigest(), len(stripped))

 
     @synchronized
     def subscribe(self, callback):
 
     @synchronized
     def subscribe(self, callback):


@@ -1099,7 +1144,7 @@ class RichCollectionBase(CollectionBase):
     @synchronized
     def flush(self):
         """Flush bufferblocks to Keep."""
     @synchronized
     def flush(self):
         """Flush bufferblocks to Keep."""

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

             e.flush()
 
 
             e.flush()
 
 


@@ -1149,12 +1194,14 @@ class Collection(RichCollectionBase):
                  parent=None,
                  apiconfig=None,
                  block_manager=None,
                  parent=None,
                  apiconfig=None,
                  block_manager=None,

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

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

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

         :parent:
           the parent Collection, may be None.
 
         :parent:
           the parent Collection, may be None.
 


@@ -1186,6 +1233,7 @@ class Collection(RichCollectionBase):
         self._keep_client = keep_client
         self._block_manager = block_manager
         self.replication_desired = replication_desired
         self._keep_client = keep_client
         self._block_manager = block_manager
         self.replication_desired = replication_desired

+        self.put_threads = put_threads

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


@@ -1195,6 +1243,7 @@ class Collection(RichCollectionBase):
         self.num_retries = num_retries if num_retries is not None else 0
         self._manifest_locator = None
         self._manifest_text = None
         self.num_retries = num_retries if num_retries is not None else 0
         self._manifest_locator = None
         self._manifest_text = None

+        self._portable_data_hash = None

         self._api_response = None
         self._past_versions = set()
 
         self._api_response = None
         self._past_versions = set()
 


@@ -1202,11 +1251,11 @@ class Collection(RichCollectionBase):
         self.events = None
 
         if manifest_locator_or_text:
         self.events = None
 
         if manifest_locator_or_text:

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

                 self._manifest_locator = manifest_locator_or_text
                 self._manifest_locator = manifest_locator_or_text

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

                 self._manifest_locator = manifest_locator_or_text
                 self._manifest_locator = manifest_locator_or_text

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

                 self._manifest_text = manifest_locator_or_text
             else:
                 raise errors.ArgumentError(
                 self._manifest_text = manifest_locator_or_text
             else:
                 raise errors.ArgumentError(


@@ -1276,7 +1325,7 @@ class Collection(RichCollectionBase):
             copies = (self.replication_desired or
                       self._my_api()._rootDesc.get('defaultCollectionReplication',
                                                    2))
             copies = (self.replication_desired or
                       self._my_api()._rootDesc.get('defaultCollectionReplication',
                                                    2))

-            self._block_manager = _BlockManager(self._my_keep(), copies=copies)
+            self._block_manager = _BlockManager(self._my_keep(), copies=copies, put_threads=self.put_threads)

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


@@ -1291,66 +1340,27 @@ class Collection(RichCollectionBase):
         # it.  If instantiation fails, we'll fall back to the except
         # clause, just like any other Collection lookup
         # failure. Return an exception, or None if successful.
         # it.  If instantiation fails, we'll fall back to the except
         # clause, just like any other Collection lookup
         # failure. Return an exception, or None if successful.

-        try:
-            self._remember_api_response(self._my_api().collections().get(
-                uuid=self._manifest_locator).execute(
-                    num_retries=self.num_retries))
-            self._manifest_text = self._api_response['manifest_text']
-            # If not overriden via kwargs, we should try to load the
-            # replication_desired from the API server
-            if self.replication_desired is None:
-                self.replication_desired = self._api_response.get('replication_desired', None)
-            return None
-        except Exception as e:
-            return e
-
-    def _populate_from_keep(self):
-        # Retrieve a manifest directly from Keep. This has a chance of
-        # working if [a] the locator includes a permission signature
-        # or [b] the Keep services are operating in world-readable
-        # mode. Return an exception, or None if successful.
-        try:
-            self._manifest_text = self._my_keep().get(
-                self._manifest_locator, num_retries=self.num_retries)
-        except Exception as e:
-            return e
+        self._remember_api_response(self._my_api().collections().get(
+            uuid=self._manifest_locator).execute(
+                num_retries=self.num_retries))
+        self._manifest_text = self._api_response['manifest_text']
+        self._portable_data_hash = self._api_response['portable_data_hash']
+        # If not overriden via kwargs, we should try to load the
+        # replication_desired from the API server
+        if self.replication_desired is None:
+            self.replication_desired = self._api_response.get('replication_desired', None)

 
     def _populate(self):
 
     def _populate(self):

-        if self._manifest_locator is None and self._manifest_text is None:
-            return
-        error_via_api = None
-        error_via_keep = None
-        should_try_keep = ((self._manifest_text is None) and
-                           util.keep_locator_pattern.match(
-                               self._manifest_locator))
-        if ((self._manifest_text is None) and
-            util.signed_locator_pattern.match(self._manifest_locator)):
-            error_via_keep = self._populate_from_keep()

         if self._manifest_text is None:
         if self._manifest_text is None:

-            error_via_api = self._populate_from_api_server()
-            if error_via_api is not None and not should_try_keep:
-                raise error_via_api
-        if ((self._manifest_text is None) and
-            not error_via_keep and
-            should_try_keep):
-            # Looks like a keep locator, and we didn't already try keep above
-            error_via_keep = self._populate_from_keep()
-        if self._manifest_text is None:
-            # Nothing worked!
-            raise errors.NotFoundError(
-                ("Failed to retrieve collection '{}' " +
-                 "from either API server ({}) or Keep ({})."
-                 ).format(
-                    self._manifest_locator,
-                    error_via_api,
-                    error_via_keep))
-        # populate
+            if self._manifest_locator is None:
+                return
+            else:
+                self._populate_from_api_server()

         self._baseline_manifest = self._manifest_text
         self._import_manifest(self._manifest_text)
 
         self._baseline_manifest = self._manifest_text
         self._import_manifest(self._manifest_text)
 

-

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

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

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


@@ -1426,7 +1436,7 @@ class Collection(RichCollectionBase):
     @must_be_writable
     @synchronized
     @retry_method
     @must_be_writable
     @synchronized
     @retry_method

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

         """Save collection to an existing collection record.
 
         Commit pending buffer blocks to Keep, merge with remote record (if
         """Save collection to an existing collection record.
 
         Commit pending buffer blocks to Keep, merge with remote record (if


@@ -1455,13 +1465,18 @@ class Collection(RichCollectionBase):
                 self.update()
 
             text = self.manifest_text(strip=False)
                 self.update()
 
             text = self.manifest_text(strip=False)

+            body={'manifest_text': text}
+            if storage_classes:
+                body["storage_classes_desired"] = storage_classes
+

             self._remember_api_response(self._my_api().collections().update(
                 uuid=self._manifest_locator,
             self._remember_api_response(self._my_api().collections().update(
                 uuid=self._manifest_locator,

-                body={'manifest_text': text}
+                body=body

                 ).execute(
                     num_retries=num_retries))
             self._manifest_text = self._api_response["manifest_text"]
                 ).execute(
                     num_retries=num_retries))
             self._manifest_text = self._api_response["manifest_text"]

-            self.set_committed()
+            self._portable_data_hash = self._api_response["portable_data_hash"]
+            self.set_committed(True)

 
         return self._manifest_text
 
 
         return self._manifest_text
 


@@ -1472,6 +1487,7 @@ class Collection(RichCollectionBase):
     def save_new(self, name=None,
                  create_collection_record=True,
                  owner_uuid=None,
     def save_new(self, name=None,
                  create_collection_record=True,
                  owner_uuid=None,

+                 storage_classes=None,

                  ensure_unique_name=False,
                  num_retries=None):
         """Save collection to a new collection record.
                  ensure_unique_name=False,
                  num_retries=None):
         """Save collection to a new collection record.


@@ -1514,17 +1530,24 @@ class Collection(RichCollectionBase):
                     "replication_desired": self.replication_desired}
             if owner_uuid:
                 body["owner_uuid"] = owner_uuid
                     "replication_desired": self.replication_desired}
             if owner_uuid:
                 body["owner_uuid"] = owner_uuid

+            if storage_classes:
+                body["storage_classes_desired"] = storage_classes

 
             self._remember_api_response(self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries))
             text = self._api_response["manifest_text"]
 
             self._manifest_locator = self._api_response["uuid"]
 
             self._remember_api_response(self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries))
             text = self._api_response["manifest_text"]
 
             self._manifest_locator = self._api_response["uuid"]

+            self._portable_data_hash = self._api_response["portable_data_hash"]

 
             self._manifest_text = text
 
             self._manifest_text = text

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

 
         return text
 
 
         return text
 

+    _token_re = re.compile(r'(\S+)(\s+|$)')
+    _block_re = re.compile(r'[0-9a-f]{32}\+(\d+)(\+\S+)*')
+    _segment_re = re.compile(r'(\d+):(\d+):(\S+)')
+

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


@@ -1543,7 +1566,7 @@ class Collection(RichCollectionBase):
         stream_name = None
         state = STREAM_NAME
 
         stream_name = None
         state = STREAM_NAME
 

-        for token_and_separator in re.finditer(r'(\S+)(\s+|$)', manifest_text):
+        for token_and_separator in self._token_re.finditer(manifest_text):

             tok = token_and_separator.group(1)
             sep = token_and_separator.group(2)
 
             tok = token_and_separator.group(1)
             sep = token_and_separator.group(2)
 


@@ -1552,25 +1575,25 @@ class Collection(RichCollectionBase):
                 stream_name = tok.replace('\\040', ' ')
                 blocks = []
                 segments = []
                 stream_name = tok.replace('\\040', ' ')
                 blocks = []
                 segments = []

-                streamoffset = 0L
+                streamoffset = 0

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

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

                 if block_locator:
                 if block_locator:

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

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

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

                 if file_segment:
                 if file_segment:

-                    pos = long(file_segment.group(1))
-                    size = long(file_segment.group(2))
+                    pos = int(file_segment.group(1))
+                    size = int(file_segment.group(2))

                     name = file_segment.group(3).replace('\\040', ' ')
                     filepath = os.path.join(stream_name, name)
                     afile = self.find_or_create(filepath, FILE)
                     name = file_segment.group(3).replace('\\040', ' ')
                     filepath = os.path.join(stream_name, name)
                     afile = self.find_or_create(filepath, FILE)


@@ -1586,7 +1609,7 @@ class Collection(RichCollectionBase):
                 stream_name = None
                 state = STREAM_NAME
 
                 stream_name = None
                 state = STREAM_NAME
 

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

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


@@ -1636,7 +1659,7 @@ class Subcollection(RichCollectionBase):
     @must_be_writable
     @synchronized
     def _reparent(self, newparent, newname):
     @must_be_writable
     @synchronized
     def _reparent(self, newparent, newname):

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

         self.flush()
         self.parent.remove(self.name, recursive=True)
         self.parent = newparent
         self.flush()
         self.parent.remove(self.name, recursive=True)
         self.parent = newparent


@@ -1647,9 +1670,8 @@ class Subcollection(RichCollectionBase):
 class CollectionReader(Collection):
     """A read-only collection object.
 
 class CollectionReader(Collection):
     """A read-only collection object.
 

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

 
     """
     def __init__(self, manifest_locator_or_text, *args, **kwargs):
 
     """
     def __init__(self, manifest_locator_or_text, *args, **kwargs):