X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/7497b21c937bb6e8451f16047945b7cfc9081a53..3513c7def7eacdeef16c355f1b9be93830dcf946:/sdk/python/arvados/arvfile.py

diff --git a/sdk/python/arvados/arvfile.py b/sdk/python/arvados/arvfile.py
index f2f7df2dce..85366d2fdc 100644
--- a/sdk/python/arvados/arvfile.py
+++ b/sdk/python/arvados/arvfile.py
@@ -10,6 +10,7 @@ import copy
 import errno
 import re
 import logging
+import collections
 
 from .errors import KeepWriteError, AssertionError, ArgumentError
 from .keep import KeepLocator
@@ -405,7 +406,7 @@ class _BlockManager(object):
     def __init__(self, keep, copies=None):
         """keep: KeepClient object to use"""
         self._keep = keep
-        self._bufferblocks = {}
+        self._bufferblocks = collections.OrderedDict()
         self._put_queue = None
         self._put_threads = None
         self._prefetch_queue = None
@@ -549,6 +550,31 @@ class _BlockManager(object):
     def __exit__(self, exc_type, exc_value, traceback):
         self.stop_threads()
 
+    @synchronized
+    def repack_small_blocks(self, force=False, sync=False):
+        """Packs small blocks together before uploading"""
+        # Search blocks ready for getting packed together before being committed to Keep.
+        small_blocks = [b for b in self._bufferblocks.values() if b.state() == _BufferBlock.WRITABLE and b.owner.closed()]
+        if len(small_blocks) <= 1:
+            # Not enough small blocks for repacking
+            return
+
+        # Check if there are enough small blocks for filling up one in full
+        pending_write_size = sum([b.size() for b in small_blocks])
+        if force or (pending_write_size >= config.KEEP_BLOCK_SIZE):
+            new_bb = _BufferBlock("bufferblock%i" % len(self._bufferblocks), 2**14, None)
+            self._bufferblocks[new_bb.blockid] = new_bb
+            size = 0
+            while len(small_blocks) > 0 and (size + small_blocks[0].size()) <= config.KEEP_BLOCK_SIZE:
+                bb = small_blocks.pop(0)
+                size += bb.size()
+                arvfile = bb.owner
+                new_bb.append(bb.buffer_view[0:bb.write_pointer].tobytes())
+                arvfile.set_segments([Range(new_bb.blockid, 0, bb.size(), size-bb.size())])
+                bb.clear()
+                del self._bufferblocks[bb.blockid]
+            self.commit_bufferblock(new_bb, sync=sync)
+
     def commit_bufferblock(self, block, sync):
         """Initiate a background upload of a bufferblock.
 
@@ -562,7 +588,6 @@ class _BlockManager(object):
           which case it will wait on an upload queue slot.
 
         """
-
         try:
             # Mark the block as PENDING so to disallow any more appends.
             block.set_state(_BufferBlock.PENDING)
@@ -629,11 +654,13 @@ class _BlockManager(object):
         are uploaded.  Raises KeepWriteError() if any blocks failed to upload.
 
         """
+        self.repack_small_blocks(force=True, sync=True)
+
         with self.lock:
             items = self._bufferblocks.items()
 
         for k,v in items:
-            if v.state() != _BufferBlock.COMMITTED:
+            if v.state() != _BufferBlock.COMMITTED and v.owner:
                 v.owner.flush(sync=False)
 
         with self.lock:
@@ -700,6 +727,7 @@ class ArvadosFile(object):
         """
         self.parent = parent
         self.name = name
+        self._writers = set()
         self._committed = False
         self._segments = []
         self.lock = parent.root_collection().lock
@@ -776,9 +804,13 @@ class ArvadosFile(object):
     def __ne__(self, other):
         return not self.__eq__(other)
 
+    @synchronized
+    def set_segments(self, segs):
+        self._segments = segs
+
     @synchronized
     def set_committed(self):
-        """Set committed flag to False"""
+        """Set committed flag to True"""
         self._committed = True
 
     @synchronized
@@ -786,6 +818,34 @@ class ArvadosFile(object):
         """Get whether this is committed or not."""
         return self._committed
 
+    @synchronized
+    def add_writer(self, writer):
+        """Add an ArvadosFileWriter reference to the list of writers"""
+        if isinstance(writer, ArvadosFileWriter):
+            self._writers.add(writer)
+
+    @synchronized
+    def remove_writer(self, writer):
+        """
+        Called from ArvadosFileWriter.close(). Remove a writer reference from the list
+        and do some block maintenance tasks.
+        """
+        self._writers.remove(writer)
+
+        if self.size() > config.KEEP_BLOCK_SIZE / 2:
+            # File writer closed, not small enough for repacking
+            self.flush()
+        elif self.closed():
+            # All writers closed and size is adequate for repacking
+            self.parent._my_block_manager().repack_small_blocks()
+
+    def closed(self):
+        """
+        Get whether this is closed or not. When the writers list is empty, the file
+        is supposed to be closed.
+        """
+        return len(self._writers) == 0
+
     @must_be_writable
     @synchronized
     def truncate(self, size):
@@ -1067,6 +1127,7 @@ class ArvadosFileWriter(ArvadosFileReader):
     def __init__(self, arvadosfile, mode, num_retries=None):
         super(ArvadosFileWriter, self).__init__(arvadosfile, num_retries=num_retries)
         self.mode = mode
+        self.arvadosfile.add_writer(self)
 
     @_FileLikeObjectBase._before_close
     @retry_method
@@ -1098,5 +1159,5 @@ class ArvadosFileWriter(ArvadosFileReader):
 
     def close(self):
         if not self.closed:
-            self.flush()
+            self.arvadosfile.remove_writer(self)
             super(ArvadosFileWriter, self).close()