Wrap FileIO, FileHandle, and VFS

Author: nguyenv

tiledb/cc/context.cc

@@ -18,7 +18,8 @@ void init_context(py::module &m) {
 
       .def_property_readonly("config", &Context::config)
       .def("set_tag", &Context::set_tag)
-      .def("get_stats", &Context::stats);
+      .def("get_stats", &Context::stats)
+      .def("is_supported_fs", &Context::is_supported_fs);
 }
 
 void init_config(py::module &m) {

tiledb/cc/enum.cc

@@ -65,6 +65,9 @@ void init_enums(py::module &m) {
   py::enum_<tiledb_vfs_mode_t>(m, "VFSMode") DVENUM(READ) DVENUM(WRITE)
       DVENUM(APPEND);
 
+  py::enum_<tiledb_filesystem_t>(m, "FileSystem") DENUM(S3) DENUM(AZURE)
+      DENUM(GCS) DENUM(HDFS);
+
   // test helpers to check enum name against typed value
   m.def("_enum_string", &tiledb::impl::type_to_str);
   m.def("_enum_string",

tiledb/cc/vfs.cc

@@ -58,7 +58,12 @@ class FileHandle {
     tiledb_vfs_open(this->_ctx, vfs.ptr().get(), uri.c_str(), mode, &this->_fh);
   }
 
-  ~FileHandle() { tiledb_vfs_close(this->_ctx, this->_fh); }
+  ~FileHandle() {
+    if (!this->closed())
+      this->close();
+  }
+
+  void close() { tiledb_vfs_close(this->_ctx, this->_fh); }
 
   py::bytes read(uint64_t offset, uint64_t nbytes) {
     py::array data = py::array(py::dtype::of<std::byte>(), nbytes);
@@ -93,6 +98,7 @@ void init_file_handle(py::module &m) {
 
       .def_property_readonly("closed", &FileHandle::closed)
 
+      .def("close", &FileHandle::close)
       .def("read", &FileHandle::read)
       .def("write", &FileHandle::write)
       .def("flush", &FileHandle::flush);

tiledb/libtiledb.pyx

@@ -14,6 +14,7 @@ from collections import OrderedDict
 
 from .ctx import default_ctx
 from .filter import FilterList
+from .vfs import VFS
 
 import tiledb.cc as lt
 
@@ -3453,7 +3454,7 @@ cdef class Array(object):
         if overwrite:
             if object_type(uri) == "array":
                 if uri.startswith("file://") or "://" not in uri:
-                    if lt.VFS().remove_dir(uri) != TILEDB_OK:
+                    if VFS().remove_dir(uri) != TILEDB_OK:
                         _raise_ctx_err(ctx_ptr, rc)
                 else:
                     raise TypeError("Cannot overwrite non-local array.")

tiledb/tests/test_libtiledb.py

@@ -3725,7 +3725,9 @@ def test_write_read(self):
         self.assertEqual(vfs.file_size(self.path("abc")), 3)
 
         fio = vfs.open(self.path("abc"), "rb")
-        with pytest.warns(DeprecationWarning, match="Use `FileIO.read`"):
+        with pytest.warns(
+            DeprecationWarning, match="Use `FileIO.seek` and `FileIO.read`"
+        ):
             self.assertEqual(vfs.read(fio, 0, 3), buffer)
         fio.close()
 
@@ -3740,7 +3742,7 @@ def test_write_read(self):
         fio.close()
 
         # read from file that does not exist
-        with self.assertRaises(tiledb.TileDBError):
+        with self.assertRaises(IOError):
             vfs.open(self.path("do_not_exist"), "rb")
 
     def test_io(self):