Extract DeletionVector logic from PuffinFile

Author: ebyhr

pyiceberg/io/pyarrow.py

@@ -147,7 +147,7 @@
 from pyiceberg.table.locations import load_location_provider
 from pyiceberg.table.metadata import TableMetadata
 from pyiceberg.table.name_mapping import NameMapping, apply_name_mapping
-from pyiceberg.table.puffin import PuffinFile
+from pyiceberg.table.update.deletion_vector import DeletionVector
 from pyiceberg.transforms import IdentityTransform, TruncateTransform
 from pyiceberg.typedef import EMPTY_DICT, Properties, Record, TableVersion
 from pyiceberg.types import (
@@ -1141,7 +1141,7 @@ def _read_deletes(io: FileIO, data_file: DataFile) -> dict[str, pa.ChunkedArray]
         with io.new_input(data_file.file_path).open() as fi:
             payload = fi.read()
 
-        return PuffinFile(payload).to_vector()
+        return DeletionVector(payload).to_vector()
     else:
         raise ValueError(f"Delete file format not supported: {data_file.file_format}")
 

pyiceberg/table/puffin.py

@@ -14,52 +14,17 @@
 # KIND, either express or implied.  See the License for the
 # specific language governing permissions and limitations
 # under the License.
-import math
 from typing import TYPE_CHECKING, Literal
 
 from pydantic import Field
-from pyroaring import BitMap, FrozenBitMap
 
 from pyiceberg.typedef import IcebergBaseModel
 
 if TYPE_CHECKING:
-    import pyarrow as pa
+    pass
 
 # Short for: Puffin Fratercula arctica, version 1
 MAGIC_BYTES = b"PFA1"
-EMPTY_BITMAP = FrozenBitMap()
-MAX_JAVA_SIGNED = int(math.pow(2, 31)) - 1
-PROPERTY_REFERENCED_DATA_FILE = "referenced-data-file"
-
-
-def _deserialize_bitmap(pl: bytes) -> list[BitMap]:
-    number_of_bitmaps = int.from_bytes(pl[0:8], byteorder="little")
-    pl = pl[8:]
-
-    bitmaps = []
-    last_key = -1
-    for _ in range(number_of_bitmaps):
-        key = int.from_bytes(pl[0:4], byteorder="little")
-        if key < 0:
-            raise ValueError(f"Invalid unsigned key: {key}")
-        if key <= last_key:
-            raise ValueError("Keys must be sorted in ascending order")
-        if key > MAX_JAVA_SIGNED:
-            raise ValueError(f"Key {key} is too large, max {MAX_JAVA_SIGNED} to maintain compatibility with Java impl")
-        pl = pl[4:]
-
-        while last_key < key - 1:
-            bitmaps.append(EMPTY_BITMAP)
-            last_key += 1
-
-        bm = BitMap().deserialize(pl)
-        # TODO: Optimize this
-        pl = pl[len(bm.serialize()) :]
-        bitmaps.append(bm)
-
-        last_key = key
-
-    return bitmaps
 
 
 class PuffinBlobMetadata(IcebergBaseModel):
@@ -78,15 +43,9 @@ class Footer(IcebergBaseModel):
     properties: dict[str, str] = Field(default_factory=dict)
 
 
-def _bitmaps_to_chunked_array(bitmaps: list[BitMap]) -> "pa.ChunkedArray":
-    import pyarrow as pa
-
-    return pa.chunked_array([(key_pos << 32) + pos for pos in bitmap] for key_pos, bitmap in enumerate(bitmaps))
-
-
 class PuffinFile:
     footer: Footer
-    _deletion_vectors: dict[str, list[BitMap]]
+    _payload: bytes
 
     def __init__(self, puffin: bytes) -> None:
         for magic_bytes in [puffin[:4], puffin[-4:]]:
@@ -105,12 +64,7 @@ def __init__(self, puffin: bytes) -> None:
         footer_payload_size_int = int.from_bytes(puffin[-12:-8], byteorder="little")
 
         self.footer = Footer.model_validate_json(puffin[-(footer_payload_size_int + 12) : -12])
-        puffin = puffin[8:]
-
-        self._deletion_vectors = {
-            blob.properties[PROPERTY_REFERENCED_DATA_FILE]: _deserialize_bitmap(puffin[blob.offset : blob.offset + blob.length])
-            for blob in self.footer.blobs
-        }
+        self._payload = puffin[8:]
 
-    def to_vector(self) -> dict[str, "pa.ChunkedArray"]:
-        return {path: _bitmaps_to_chunked_array(bitmaps) for path, bitmaps in self._deletion_vectors.items()}
+    def get_blob_payload(self, blob: PuffinBlobMetadata) -> bytes:
+        return self._payload[blob.offset : blob.offset + blob.length]

pyiceberg/table/update/deletion_vector.py

@@ -0,0 +1,79 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+import math
+from typing import TYPE_CHECKING
+
+from pyroaring import BitMap, FrozenBitMap
+
+from pyiceberg.table.puffin import PuffinFile
+
+if TYPE_CHECKING:
+    import pyarrow as pa
+
+EMPTY_BITMAP = FrozenBitMap()
+MAX_JAVA_SIGNED = int(math.pow(2, 31)) - 1
+PROPERTY_REFERENCED_DATA_FILE = "referenced-data-file"
+
+
+class DeletionVector:
+    _deletion_vectors: dict[str, list[BitMap]]
+
+    def __init__(self, puffin: bytes) -> None:
+        puffin_file = PuffinFile(puffin)
+        self._deletion_vectors = {
+            blob.properties[PROPERTY_REFERENCED_DATA_FILE]: self._deserialize_bitmap(puffin_file.get_blob_payload(blob))
+            for blob in puffin_file.footer.blobs
+        }
+
+    @staticmethod
+    def _deserialize_bitmap(pl: bytes) -> list[BitMap]:
+        number_of_bitmaps = int.from_bytes(pl[0:8], byteorder="little")
+        pl = pl[8:]
+
+        bitmaps = []
+        last_key = -1
+        for _ in range(number_of_bitmaps):
+            key = int.from_bytes(pl[0:4], byteorder="little")
+            if key < 0:
+                raise ValueError(f"Invalid unsigned key: {key}")
+            if key <= last_key:
+                raise ValueError("Keys must be sorted in ascending order")
+            if key > MAX_JAVA_SIGNED:
+                raise ValueError(f"Key {key} is too large, max {MAX_JAVA_SIGNED} to maintain compatibility with Java impl")
+            pl = pl[4:]
+
+            while last_key < key - 1:
+                bitmaps.append(EMPTY_BITMAP)
+                last_key += 1
+
+            bm = BitMap().deserialize(pl)
+            # TODO: Optimize this
+            pl = pl[len(bm.serialize()) :]
+            bitmaps.append(bm)
+
+            last_key = key
+
+        return bitmaps
+
+    @staticmethod
+    def _bitmaps_to_chunked_array(bitmaps: list[BitMap]) -> "pa.ChunkedArray":
+        import pyarrow as pa
+
+        return pa.chunked_array([(key_pos << 32) + pos for pos in bitmap] for key_pos, bitmap in enumerate(bitmaps))
+
+    def to_vector(self) -> dict[str, "pa.ChunkedArray"]:
+        return {path: self._bitmaps_to_chunked_array(bitmaps) for path, bitmaps in self._deletion_vectors.items()}

tests/table/test_puffin.py tests/table/test_deletion_vector.pytests/table/test_puffin.py renamed to tests/table/test_deletion_vector.py

@@ -19,7 +19,7 @@
 import pytest
 from pyroaring import BitMap
 
-from pyiceberg.table.puffin import _deserialize_bitmap
+from pyiceberg.table.update.deletion_vector import DeletionVector
 
 
 def _open_file(file: str) -> bytes:
@@ -32,7 +32,7 @@ def test_map_empty() -> None:
     puffin = _open_file("64mapempty.bin")
 
     expected: list[BitMap] = []
-    actual = _deserialize_bitmap(puffin)
+    actual = DeletionVector._deserialize_bitmap(puffin)
 
     assert expected == actual
 
@@ -41,7 +41,7 @@ def test_map_bitvals() -> None:
     puffin = _open_file("64map32bitvals.bin")
 
     expected = [BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])]
-    actual = _deserialize_bitmap(puffin)
+    actual = DeletionVector._deserialize_bitmap(puffin)
 
     assert expected == actual
 
@@ -61,7 +61,7 @@ def test_map_spread_vals() -> None:
         BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]),
         BitMap([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]),
     ]
-    actual = _deserialize_bitmap(puffin)
+    actual = DeletionVector._deserialize_bitmap(puffin)
 
     assert expected == actual
 
@@ -70,4 +70,4 @@ def test_map_high_vals() -> None:
     puffin = _open_file("64maphighvals.bin")
 
     with pytest.raises(ValueError, match="Key 4022190063 is too large, max 2147483647 to maintain compatibility with Java impl"):
-        _ = _deserialize_bitmap(puffin)
+        _ = DeletionVector._deserialize_bitmap(puffin)