Implement serialization functionality for Config and VFS objects (#2110)

* Implement serialization functionality for VFS objects
* Implement serialization for Config
* Remove PatchedConfig and PatchedCtx

---------

Co-authored-by: Theodore Tsirpanis <[email protected]>

Author: kounelisagis

tiledb/ctx.py

@@ -293,6 +293,20 @@ def save(self, uri: str):
         """
         self.save_to_file(uri)
 
+    def __reduce__(self):
+        """
+        Customize the pickling process by defining how to serialize
+        and reconstruct the Config object.
+        """
+        state = self.dict()
+        return (self.__class__, (), state)
+
+    def __setstate__(self, state):
+        """
+        Customize how the Config object is restored from its serialized state.
+        """
+        self.__init__(state)
+
 
 class ConfigKeys:
     """

tiledb/tests/conftest.py

@@ -52,54 +52,6 @@ def pytest_configure(config):
     # default must be set here rather than globally
     pytest.tiledb_vfs = "file"
 
-    vfs_config(config)
-
-
-def vfs_config(pytestconfig):
-    vfs_config_override = {}
-
-    vfs = pytestconfig.getoption("vfs")
-    if vfs == "s3":
-        pytest.tiledb_vfs = "s3"
-
-        vfs_config_override.update(
-            {
-                "vfs.s3.endpoint_override": "localhost:9999",
-                "vfs.s3.aws_access_key_id": "minio",
-                "vfs.s3.aws_secret_access_key": "miniosecretkey",
-                "vfs.s3.scheme": "https",
-                "vfs.s3.verify_ssl": False,
-                "vfs.s3.use_virtual_addressing": False,
-            }
-        )
-
-    vfs_config_arg = pytestconfig.getoption("vfs-config", None)
-    if vfs_config_arg:
-        pass
-
-    tiledb._orig_ctx = tiledb.Ctx
-
-    def get_config(config):
-        final_config = {}
-        if isinstance(config, tiledb.Config):
-            final_config = config.dict()
-        elif config:
-            final_config = config
-
-        final_config.update(vfs_config_override)
-        return final_config
-
-    class PatchedCtx(tiledb.Ctx):
-        def __init__(self, config=None):
-            super().__init__(get_config(config))
-
-    class PatchedConfig(tiledb.Config):
-        def __init__(self, params=None):
-            super().__init__(get_config(params))
-
-    tiledb.Ctx = PatchedCtx
-    tiledb.Config = PatchedConfig
-
 
 @pytest.fixture(scope="function", autouse=True)
 def isolate_os_fork(original_os_fork):

tiledb/tests/test_context_and_config.py

@@ -1,4 +1,6 @@
+import io
 import os
+import pickle
 import subprocess
 import sys
 import xml
@@ -261,3 +263,20 @@ def test_config_repr_html(self):
             pytest.fail(
                 f"Could not parse config._repr_html_(). Saw {config._repr_html_()}"
             )
+
+    def test_config_pickle(self):
+        # test that Config can be pickled and unpickled
+        config = tiledb.Config(
+            {
+                "rest.use_refactored_array_open": "false",
+                "rest.use_refactored_array_open_and_query_submit": "true",
+                "vfs.azure.storage_account_name": "myaccount",
+            }
+        )
+        with io.BytesIO() as buf:
+            pickle.dump(config, buf)
+            buf.seek(0)
+            config2 = pickle.load(buf)
+
+            self.assertIsInstance(config2, tiledb.Config)
+            self.assertEqual(config2.dict(), config.dict())

tiledb/tests/test_vfs.py

@@ -1,6 +1,7 @@
 import io
 import os
 import pathlib
+import pickle
 import random
 import sys
 
@@ -239,6 +240,21 @@ def test_io(self):
             txtio = io.TextIOWrapper(f2, encoding="utf-8")
             self.assertEqual(txtio.readlines(), lines)
 
+    def test_pickle(self):
+        # test that vfs can be pickled and unpickled with config options
+        config = tiledb.Config(
+            {"vfs.s3.region": "eu-west-1", "vfs.max_parallel_ops": "1"}
+        )
+        vfs = tiledb.VFS(config)
+        with io.BytesIO() as buf:
+            pickle.dump(vfs, buf)
+            buf.seek(0)
+            vfs2 = pickle.load(buf)
+
+            self.assertIsInstance(vfs2, tiledb.VFS)
+            self.assertEqual(vfs2.config()["vfs.s3.region"], "eu-west-1")
+            self.assertEqual(vfs2.config()["vfs.max_parallel_ops"], "1")
+
     def test_sc42569_vfs_memoryview(self):
         # This test is to ensure that giving np.ndarray buffer to readinto works
         # when trying to write bytes that cannot be converted to float32 or int32

tiledb/vfs.py

@@ -25,7 +25,7 @@ class VFS(lt.VFS):
     """
 
     def __init__(self, config: Union[Config, dict] = None, ctx: Optional[Ctx] = None):
-        ctx = ctx or default_ctx()
+        self.ctx = ctx or default_ctx()
 
         if config:
             from .libtiledb import Config
@@ -39,12 +39,12 @@ def __init__(self, config: Union[Config, dict] = None, ctx: Optional[Ctx] = None
                     raise ValueError("`config` argument must be of type Config or dict")
 
             # Convert all values to strings
-            config = {k: str(v) for k, v in config.items()}
+            self.config_dict = {k: str(v) for k, v in config.items()}
 
-            ccfg = tiledb.Config(config)
-            super().__init__(ctx, ccfg)
+            ccfg = tiledb.Config(self.config_dict)
+            super().__init__(self.ctx, ccfg)
         else:
-            super().__init__(ctx)
+            super().__init__(self.ctx)
 
     def ctx(self) -> Ctx:
         """
@@ -329,6 +329,21 @@ def touch(self, uri: _AnyPath):
     isfile = is_file
     size = file_size
 
+    # pickling support
+    def __getstate__(self):
+        # self.config_dict might not exist. In that case use the config from ctx.
+        if hasattr(self, "config_dict"):
+            config_dict = self.config_dict
+        else:
+            config_dict = self.config().dict()
+        return (config_dict,)
+
+    def __setstate__(self, state):
+        config_dict = state[0]
+        config = Config(params=config_dict)
+        ctx = Ctx(config)
+        self.__init__(config=config, ctx=ctx)
+
 
 class FileIO(io.RawIOBase):
     """TileDB FileIO class that encapsulates files opened by tiledb.VFS. The file