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Virtual Filesystem
TileDB is designed such that all IO to/from the storage backends is abstracted behind a Virtual Filesystem (VFS) module. This module supports simple operations, such as creating a file/directory, reading/writing to a file, etc. This abstraction enables us to easily plug in more storage backends in the future, effectively making the storage backend opaque to the user.
A nice positive “by-product” of this architecture is that it is possible to expose the basic virtual filesystem functionality via the TileDB APIs. This provides a simplified interface for file IO and directory management (i.e., not related to TileDB objects such as array) on all the storage backends that TileDB supports.
This page covers most of the TileDB VFS functionality.
Writing
C
C++
Python
R
Java
Go
1
// Create TileDB context
2
tiledb_ctx_t* ctx;
3
tiledb_ctx_alloc(NULL, &ctx);
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// Create TileDB VFS
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tiledb_vfs_t* vfs;
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tiledb_vfs_alloc(ctx, NULL, &vfs);
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// Write binary data
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tiledb_vfs_fh_t* fh;
11
tiledb_vfs_open(ctx, vfs, "tiledb_vfs.bin", TILEDB_VFS_WRITE, &fh);
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float f1 = 153.0;
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const char* s1 = "abcd";
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tiledb_vfs_write(ctx, fh, &f1, sizeof(float));
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tiledb_vfs_write(ctx, fh, s1, strlen(s1));
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tiledb_vfs_close(ctx, fh);
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tiledb_vfs_fh_free(&fh);
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// Write binary data again - this will overwrite the previous file
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tiledb_vfs_open(ctx, vfs, "tiledb_vfs.bin", TILEDB_VFS_WRITE, &fh);
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const char* s2 = "abcdef";
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f1 = 153.1;
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tiledb_vfs_write(ctx, fh, &f1, sizeof(float));
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tiledb_vfs_write(ctx, fh, s2, strlen(s2));
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tiledb_vfs_close(ctx, fh);
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tiledb_vfs_fh_free(&fh);
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// Append binary data to existing file
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tiledb_vfs_open(ctx, vfs, "tiledb_vfs.bin", TILEDB_VFS_APPEND, &fh);
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const char* s3 = "ghijkl";
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tiledb_vfs_write(ctx, fh, s3, strlen(s3));
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tiledb_vfs_close(ctx, fh);
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tiledb_vfs_fh_free(&fh);
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// Clean up
36
tiledb_vfs_free(&vfs);
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tiledb_ctx_free(&ctx);
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1
// Create TileDB context
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Context ctx;
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// Create TileDB VFS
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VFS vfs(ctx);
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// Create VFS file buffer
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VFS::filebuf fbuf(vfs);
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// Write binary data
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fbuf.open("tiledb_vfs.bin", std::ios::out);
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std::ostream os(&fbuf);
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if (!os.good()) {
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std::cerr << "Error opening file 'tiledb_vfs_bin'.\n";
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return;
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}
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float f1 = 153.0;
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std::string s1 = "abcd";
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os.write((char*)&f1, sizeof(f1));
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os.write(s1.data(), s1.size());
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// Write binary data again - this will overwrite the previous file
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fbuf.open("tiledb_vfs.bin", std::ios::out);
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if (!os.good()) {
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std::cerr << "Error opening file 'tiledb_vfs.bin' for write.\n";
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return;
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}
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f1 = 153.1;
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s1 = "abcdef";
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os.write((char*)&f1, sizeof(f1));
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os.write(s1.data(), s1.size());
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// Append binary data to existing file (this will NOT work on S3)
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fbuf.open("tiledb_vfs.bin", std::ios::app);
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if (!os.good()) {
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std::cerr << "Error opening file 'tiledb_vfs.bin' for append.\n";
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return;
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}
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s1 = "ghijkl";
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os.write(s1.data(), s1.size());
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1
# Note: the Python VFS API currently supports bytes (no automatic conversion)
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# therefore encoding must be handled manually (see calls to 'encode'
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# and 'struct.pack' below)
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import struct
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ctx = tiledb.Ctx()
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vfs = tiledb.VFS(ctx=ctx)
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# Create and open writable buffer object
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fh = vfs.open("tiledb_vfs.bin", 'w')
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vfs.write(fh, struct.pack('<f', 153.0))
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vfs.write(fh, "abcd".encode('UTF-8'))
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# Write data again - this will overwrite the previous file
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fh = vfs.open("tiledb_vfs.bin", 'w')
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vfs.write(fh, struct.pack('<f', 153.1))
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vfs.write(fh, "abcdef".encode("UTF-8"))
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# Append data to existing file (this will NOT work on S3)
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fh = vfs.open("tiledb_vfs.bin", 'a')
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vfs.write(fh, "ghijkl".encode("UTF-8"))
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# Close the handle
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vfs.close(fh)
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1
# binary file to be written
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binfile <- "tiledb_vfs.bin"
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# open file
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fhbuf <- tiledb_vfs_open(uri, "WRITE")
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# create a binary payload from a serialized R object
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payload <- as.integer(serialize(list(dbl=153, string="abcde"), NULL))
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# write it and close file
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tiledb_vfs_write(fhbuf, payload)
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tiledb_vfs_close(fhbuf)
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# write again overwriting previous write
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fhbuf <- tiledb_vfs_open(uri, "WRITE")
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payload <- as.integer(serialize(list(dbl=153.1, string="abcdef"), NULL))
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tiledb_vfs_write(fhbuf, payload)
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tiledb_vfs_close(fhbuf)
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# append to existing file
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fhbuf <- tiledb_vfs_open(uri, "APPEND")
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payload <- as.integer(serialize(c(string="ghijkl"), NULL))
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tiledb_vfs_write(fhbuf, payload)
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tiledb_vfs_close(fhbuf)
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1
// Create TileDB context and VFS
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try (Context ctx = new Context(); VFS vfs = new VFS(ctx)) {
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String sourcePath = "tiledb_vfs.bin";
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// Write binary data
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vfs.write(sourcePath, ByteBuffer.allocate(4).putFloat(153.0).array());
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byte[] resultBytes = vfs.readAllBytes(sourcePath);
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// append bytes
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String s1 = "abcd";
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vfs.write(sourcePath, s1.getBytes(), VFSMode.TILEDB_VFS_APPEND);
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// Write binary data again - this will overwrite the previous file
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vfs.write(sourcePath, ByteBuffer.allocate(4).putFloat(153.0).array(), VFSMode.TILEDB_VFS_WRITE);
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s1 = "abcdef";
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vfs.write(sourcePath, s1.getBytes(), VFSMode.TILEDB_VFS_APPEND);
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// Append binary data to existing file (this will NOT work on S3)
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s1 = "ghijkl";
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vfs.write(sourcePath, s1.getBytes(), VFSMode.TILEDB_VFS_APPEND);
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resultBytes = vfs.readAllBytes(sourcePath);
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}
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1
// Create TileDB context
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config, _ := NewConfig()
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ctx, _ := NewContext(config)
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// Create TileDB VFS
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vfs, _ := NewVFS(ctx, config)
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// Write binary data
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fh1, _ := vfs.Open("tiledb_vfs.bin", tiledb.TILEDB_VFS_WRITE)
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var f1 float32 = 153.0
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s1 := "abcd"
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vfs.Write(fh1, float32ToBytes(f1))
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vfs.Write(fh1, []byte(s1))
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vfs.Close(fh1)
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// Write binary data again - this will overwrite the previous file
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fh2, _ := vfs.Open("tiledb_vfs.bin", tiledb.TILEDB_VFS_WRITE)
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var f2 float32 = 153.1
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s2 := "abcdef"
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vfs.Write(fh2, float32ToBytes(f2))
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vfs.Write(fh2, []byte(s2))
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vfs.Close(fh2)
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// Append binary data to existing file
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fh3, _ := vfs.Open("tiledb_vfs.bin", tiledb.TILEDB_VFS_APPEND)
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s3 := "ghijkl"
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vfs.Write(fh3, []byte(s3))
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vfs.Close(fh3)
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// Clean up
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vfs.Free()
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ctx.Free()
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func float32ToBytes(float float32) []byte {
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bits := math.Float32bits(float)
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bytes := make([]byte, 4)
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binary.LittleEndian.PutUint32(bytes, bits)
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return bytes
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}
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Reading
C
C++
Python
R
Java
Go
1
// Create TileDB context
2
tiledb_ctx_t* ctx;
3
tiledb_ctx_alloc(NULL, &ctx);
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// Create TileDB VFS
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tiledb_vfs_t* vfs;
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tiledb_vfs_alloc(ctx, NULL, &vfs);
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// Read binary data
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tiledb_vfs_fh_t* fh;
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tiledb_vfs_open(ctx, vfs, "tiledb_vfs.bin", TILEDB_VFS_READ, &fh);
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float f1;
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char s1[13];
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s1[12] = '\0';
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tiledb_vfs_read(ctx, fh, 0, &f1, sizeof(float));
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tiledb_vfs_read(ctx, fh, sizeof(float), s1, 12);
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printf("Binary read:\n%.1f\n%s\n", f1, s1);
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// Clean up
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tiledb_vfs_fh_free(&fh);
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tiledb_vfs_free(&vfs);
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tiledb_ctx_free(&ctx);
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1
// Create TileDB context
2
Context ctx;
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// Create TileDB VFS
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VFS vfs(ctx);
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// Read binary data
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VFS::filebuf sbuf(vfs);
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sbuf.open("tiledb_vfs.bin", std::ios::in);
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std::istream is(&sbuf);
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if (!is.good()) {
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std::cerr << "Error opening file 'tiledb_vfs.bin'.\n";
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return;
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}
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float f1;
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std::string s1;
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auto s1_size = vfs.file_size("tiledb_vfs.bin") - sizeof(float);
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s1.resize(s1_size);
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is.read((char*)&f1, sizeof(f1));
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is.read((char*)s1.data(), 12);
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std::cout << "Binary read:\n" << f1 << '\n' << s1 << '\n';
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1
import struct
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ctx = tiledb.Ctx()
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vfs = tiledb.VFS(ctx=ctx)
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# Create and open readable handle
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fh = vfs.open("tiledb_vfs.bin", "r")
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float_struct = struct.Struct('<f')
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float_data = vfs.read(fh, 0, float_struct.size)
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string_data = vfs.read(fh, float_struct.size, 12)
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print(float_struct.unpack(float_data)[0])
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print(string_data.decode("UTF-8"))
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vfs.close(fh)
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1
# open a binary file for reading
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fhbuf <- tiledb_vfs_open(uri, "READ")
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vec <- tiledb_vfs_read(fhbuf, as.integer64(0), as.integer64(488))
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tiledb_vfs_close(fhbuf)
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print(str(unserialize(as.raw(vec))))
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1
// Create TileDB context and VFS
2
try (Context ctx = new Context(); VFS vfs = new VFS(ctx)) {
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String sourcePath = "tiledb_vfs.bin";
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byte[] resultBytes = vfs.readAllBytes(sourcePath);
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float f1 = ByteBuffer.wrap(resultBytes).order(ByteOrder.LITTLE_ENDIAN).getFloat();
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resultBytes = copyOfRange(resultBytes, 4, resultBytes.length);
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String s1 = new String( bytes, StandardCharsets.UTF_8 );
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System.out.printf("Binary read:%f\n,%s\n", f1, s1);
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}
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1
// Create TileDB context
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config, _ := NewConfig()
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ctx, _ := NewContext(config)
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// Create TileDB VFS
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vfs, _ := NewVFS(ctx, config)
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// Read binary data
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vfs.Open("tiledb_vfs.bin", tiledb.TILEDB_VFS_READ)
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sizeOfFile, _ := vfs.FileSize(vfsFileName)
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var f float32 = 0.0
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sizeOfFloat32 := uint64(unsafe.Sizeof(f))
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f1, _ := vfs.Read(fh, 0, sizeOfFloat32)
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s1, _ := vfs.Read(fh, sizeOfFloat32, sizeOfFile-sizeOfFloat32)
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fmt.Println("Binary read:")
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fmt.Println(float32FromBytes(f1))
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fmt.Println(string(s1))
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// Clean up
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vfs.Close(fh)
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vfs.Free()
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ctx.Free()
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func float32FromBytes(bytes []byte) float32 {
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bits := binary.LittleEndian.Uint32(bytes)
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float := math.Float32frombits(bits)
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return float
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}
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Managing
C
C++
Python
R
Java
Go
1
// Create TileDB context
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tiledb_ctx_t* ctx;
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tiledb_ctx_alloc(NULL, &ctx);
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// Create TileDB VFS
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tiledb_vfs_t* vfs;
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tiledb_vfs_alloc(ctx, NULL, &vfs);
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// Create directory
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int is_dir = 0;
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tiledb_vfs_is_dir(ctx, vfs, "dir_A", &is_dir);
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if (!is_dir) {
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tiledb_vfs_create_dir(ctx, vfs, "dir_A");
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printf("Created 'dir_A'\n");
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} else {
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printf("'dir_A' already exists\n");
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}
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// Creating an (empty) file
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int is_file = 0;
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tiledb_vfs_is_file(ctx, vfs, "dir_A/file_A", &is_file);
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if (!is_file) {
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tiledb_vfs_touch(ctx, vfs, "dir_A/file_A");
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printf("Created empty file 'dir_A/file_A'\n");
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} else {
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printf("'dir_A/file_A' already exists\n");
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}
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// Getting the file size
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uint64_t file_size;
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tiledb_vfs_file_size(ctx, vfs, "dir_A/file_A", &file_size);
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// Moving files (moving directories is similar)
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tiledb_vfs_move_file(ctx, vfs, "dir_A/file_A", "dir_A/file_B");
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// Deleting files and directories. Note that, in the case of directories,
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// the function will delete all the contents of the directory (i.e., it
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// works even for non-empty directories).
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tiledb_vfs_remove_file(ctx, vfs, "dir_A/file_B");
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tiledb_vfs_remove_dir(ctx, vfs, "dir_A");
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// Clean up
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tiledb_vfs_free(&vfs);
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tiledb_ctx_free(&ctx);
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1
// Create TileDB context
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Context ctx;
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// Create TileDB VFS
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VFS vfs(ctx);
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// Create directory
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if (!vfs.is_dir("dir_A")) {
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vfs.create_dir("dir_A");
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std::cout << "Created 'dir_A'\n";
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} else {
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std::cout << "'dir_A' already exists\n";
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}
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// Creating an (empty) file
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if (!vfs.is_file("dir_A/file_A")) {
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vfs.touch("dir_A/file_A");
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std::cout << "Created empty file 'dir_A/file_A'\n";
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} else {
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std::cout << "'dir_A/file_A' already exists\n";
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}
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// Getting the file size
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std::cout << "Size of file 'dir_A/file_A': " << vfs.file_size("dir_A/file_A")
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<< "\n";
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// Moving files (moving directories is similar)
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vfs.move_file("dir_A/file_A", "dir_A/file_B");
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// Deleting files and directories
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vfs.remove_file("dir_A/file_B");
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vfs.remove_dir("dir_A");
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1
import tiledb
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3
ctx = tiledb.Ctx()
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vfs = tiledb.VFS(ctx=ctx)
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# Creating a directory
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if not vfs.is_dir("dir_A"):
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vfs.create_dir("dir_A")
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print("Created 'dir_A'")
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else:
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print ("'dir_A' already exists")
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# Creating an (empty) file
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if not vfs.is_file("dir_A/file_A"):
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vfs.touch("dir_A/file_A")
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print("Created empty file 'dir_A/file_A'")
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else:
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print("'dir_A/file_A' already exists")
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# Getting the file size
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print("Size of file 'dir_A/file_A': ", vfs.file_size("dir_A/file_A"))
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# Moving files (moving directories is similar)
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vfs.move_file("dir_A/file_A", "dir_A/file_B")
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vfs.remove_file("dir_A/file_B")
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vfs.remove_dir("dir_A")
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1
library(tiledb)
2
3
ctx <- tiledb_get_context()
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vfs <- tiledb_vfs(ctx=ctx)
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## Creating a directory
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if (!tiledb_vfs_is_dir(vfs, "dir_A")) {
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tiledb_vfs_create_dir(vfs, "dir_A")
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cat("Created 'dir_A'\n")
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} else {
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cat("'dir_A' already exists\n")
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}
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## Creating an (empty) file
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if (!tiledb_vfs_is_file(vfs, "dir_A/file_A")) {
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tiledb_vfs_touch(vfs, "dir_A/file_A")
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cat("Created empty file 'dir_A/file_A'\n")
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} else {
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cat("File 'dir_A/file_A' already existed\n")
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}
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## Getting the file size
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cat("Size of file 'dir_A/file_A': ",
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tiledb_vfs_file_size(vfs, "dir_A/file_A"), "\n")
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## Moving files (moving directories is similar)
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tiledb_vfs_move_file(vfs, "dir_A/file_A", "dir_A/file_B")
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## Cleaning up
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tiledb_vfs_remove_file(vfs, "dir_A/file_B")
31
tiledb_vfs_remove_dir(vfs, "dir_A")
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1
// Create TileDB context and VFS
2
try (Context ctx = new Context(); VFS vfs = new VFS(ctx)) {
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// Create directory
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if (!vfs.isDirectory("dir_A")) {
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vfs.createDirectory("dir_A");
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System.out.println( "Created 'dir_A'");
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} else {
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System.out.println("'dir_A' already exists");
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}
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// Creating an (empty) file
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if (!vfs.isFile("dir_A/file_A")) {
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vfs.createFile("dir_A/file_A");
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System.out.println("Created empty file 'dir_A/file_A'");
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} else {
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System.out.println("'dir_A/file_A' already exists");
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}
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// Getting the file size
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System.out.printf("Size of file 'dir_A/file_A': %d\n" , vfs.fileSize("dir_A/file_A"));
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// Moving files (moving directories is similar)
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vfs.moveFile("dir_A/file_A", "dir_A/file_B");
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// Deleting files and directories
26
vfs.removeFile("dir_A/file_B");
27
vfs.removeDirectory("dir_A");
28
}
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1
// Create TileDB context
2
config, _ := NewConfig()
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ctx, _ := NewContext(config)
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// Create TileDB VFS
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vfs, _ := NewVFS(ctx, config)
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// Create directory
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vfs.CreateDir("dir_A")
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isDir, _ := vfs.IsDir("dir_A")
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if !is_dir {
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tiledb_vfs_create_dir(ctx, vfs, "dir_A")
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fmt.Println("Created 'dir_A'\n")
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} else {
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fmt.Println("'dir_A' already exists\n")
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}
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// Creating an (empty) file
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isFile, _ := vfs.IsFile("dir_A/file_A")
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if !isFile {
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vfs.Touch("dir_A/file_A")
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fmt.Println("Created empty file 'dir_A/file_A'\n")
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} else {
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fmt.Println("'dir_A/file_A' already exists\n")
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}
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// Getting the file size
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fileSize, _ := vfs.FileSize("dir_A/file_A")
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// Moving files (moving directories is similar)
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vfs.MoveFile("dir_A/file_A", "dir_A/file_B")
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// Deleting files and directories. Note that, in the case of directories,
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// the function will delete all the contents of the directory (i.e., it
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// works even for non-empty directories).
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vfs.RemoveFile(ctx, vfs, "dir_A/file_B")
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vfs.RemoveDir(ctx, vfs, "dir_A")
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39
// Clean up
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vfs.Free()
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ctx.Free()
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TileDB allows you to create/delete S3 buckets via its VFS functionality,
C
C++
Python
R
Java
Go
1
// ... create context ctx
2
// ... create VFS vfs
3
4
tiledb_vfs_create_bucket(ctx, vfs, "s3://my_bucket");
5
tiledb_vfs_remove_bucket(ctx, vfs, "s3://my_bucket");
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1
// ... create context ctx
2
// ... create VFS vfs
3
4
vfs.create_bucket("s3://my_bucket");
5
vfs.remove_bucket("s3://my_bucket");
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1
# ... create context ctx
2
# ... create VFS vfs
3
4
vfs.create_bucket("s3://my_bucket")
5
vfs.remove_bucket("s3://my_bucket")
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1
# ... create context ctx
2
# ... create VFS vfs
3
4
tiledb_vfs_create_bucket(vfs, "s3://my_bucket")
5
tiledb_vfs_remove_bucket(vfs, "s3://my_bucket")
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1
// Create TileDB context and VFS
2
try (Context ctx = new Context(); VFS vfs = new VFS(ctx)) {
3
vfs.createBucket("s3://my_bucket");
4
vfs.removeBucket("s3://my_bucket");
5
}
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1
// ... create VFS vfs
2
3
vfs.CreateBucket("s3://my_bucket")
4
vfs.RemoveBucket("s3://my_bucket")
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However, extreme care must be taken when creating/deleting buckets on AWS S3. After its creation, a bucket may take some time to “appear” in the system. This will cause problems if the user creates the bucket and immediately tries to write a file in it. Similarly, deleting a bucket may not take effect immediately and, therefore, it may continue to “exist” for some time.
Configuring VFS
You can configure VFS by passing a configuration object upon its creation.
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// Create TileDB context
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tiledb_ctx_t* ctx;
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tiledb_ctx_alloc(NULL, &ctx);
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// Create a configuration object
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tiledb_config_t *config;
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tiledb_config_alloc(&config, NULL);
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tiledb_config_set(config, "vfs.file.max_parallel_ops", "16", NULL);
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// Create TileDB VFS with a config object
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tiledb_vfs_t* vfs;
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tiledb_vfs_alloc(ctx, config, &vfs);
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// Clean up
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tiledb_config_free(&config);
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tiledb_vfs_free(&vfs);
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tiledb_ctx_free(&ctx);
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// Create TileDB context
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Context ctx;
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// Create a configuration object
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Config config;
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config["vfs.file.max_parallel_ops"] = "16";
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// Create TileDB VFS with a config object
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VFS vfs(ctx, config);
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ctx = tiledb.Ctx()
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config = tiledb.Config()
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config["vfs.file.max_parallel_ops"] = 16
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vfs = tiledb.VFS(ctx=ctx, config=config)
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# Or create the Config first and pass to the Ctx constructor
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ctx <- tiledb_get_context()
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config <- tiledb_config()
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config["vfs.file.max_parallel_ops"] <- 16
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vfs <- tiledb_vfs(config, ctx)
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## Or create the Config first and pass to the Ctx constructor
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// Create TileDB context
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try(Context ctx = new Context()) {
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HashMap<String, String> settings = new HashMap<>();
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// Set values
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settings.put("vfs.file.max_parallel_ops", "16");
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// Create TileDB VFS with a config object
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try (Config config = new Config(settings), VFS vfs = new VFS(ctx, config);) {
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}
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}
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// Create a configuration object
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config, _ := tiledb.NewConfig()
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// Create TileDB context
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ctx, _ := tiledb.NewContext(config)
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// Set vfs param
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configCtx, err := ctx.Config()
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configCtx.Set("vfs.file.max_parallel_ops", "16")
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// Create TileDB VFS with a config object
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vfs, _ := tiledb.NewVFS(ctx, config)
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// Clean up
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config.Free()
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vfs.Free()
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ctx.Free()
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If you do not set a configuration object to VFS, then VFS will inherit the (default or set) configuration of the context. Otherwise, the set options in the passed configuration object will override those of the context's, but the rest of the options will still be inherited from the context's configuration.
Last modified 1yr ago
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