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unit-capi-sparse_array.cc
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unit-capi-sparse_array.cc
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/**
* @file unit-capi-sparse_array.cc
*
* @section LICENSE
*
* The MIT License
*
* @copyright Copyright (c) 2017-2021 TileDB Inc.
* @copyright Copyright (c) 2016 MIT and Intel Corporation
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*
* @section DESCRIPTION
*
* Tests of C API for sparse array operations.
*/
#include "catch.hpp"
#include "test/src/helpers.h"
#include "test/src/vfs_helpers.h"
#ifdef _WIN32
#include "tiledb/sm/filesystem/win.h"
#else
#include "tiledb/sm/filesystem/posix.h"
#endif
#include "tiledb/sm/c_api/tiledb.h"
#include "tiledb/sm/enums/encryption_type.h"
#include "tiledb/sm/misc/utils.h"
#include "test/src/helpers.h"
#include <cassert>
#include <cstring>
#include <ctime>
#include <iostream>
#include <map>
#include <sstream>
#include <thread>
using namespace tiledb::test;
const uint64_t DIM_DOMAIN[4] = {1, 4, 1, 4};
struct SparseArrayFx {
// Constant parameters
std::string ATTR_NAME = "a";
const char* DIM1_NAME = "x";
const char* DIM2_NAME = "y";
const tiledb_datatype_t ATTR_TYPE = TILEDB_INT32;
const tiledb_datatype_t DIM_TYPE = TILEDB_INT64;
const tiledb_array_type_t ARRAY_TYPE = TILEDB_SPARSE;
int COMPRESSION_LEVEL = -1;
int ITER_NUM = 5;
const std::string ARRAY = "sparse_array";
tiledb_encryption_type_t encryption_type = TILEDB_NO_ENCRYPTION;
const char* encryption_key = nullptr;
// TileDB context
tiledb_ctx_t* ctx_;
tiledb_vfs_t* vfs_;
// Vector of supported filsystems
const std::vector<std::unique_ptr<SupportedFs>> fs_vec_;
// Functions
SparseArrayFx();
~SparseArrayFx();
void create_sparse_array(
const std::string& array_name,
tiledb_layout_t layout = TILEDB_ROW_MAJOR,
const uint64_t* dim_domain = DIM_DOMAIN);
void check_sparse_array_unordered_with_duplicates_error(
const std::string& array_name);
void check_sparse_array_unordered_with_duplicates_no_check(
const std::string& array_name);
void check_sparse_array_unordered_with_duplicates_dedup(
const std::string& array_name);
void check_sparse_array_unordered_with_all_duplicates_dedup(
const std::string& array_name);
void check_sparse_array_global_with_duplicates_error(
const std::string& array_name);
void check_sparse_array_global_with_duplicates_no_check(
const std::string& array_name);
void check_sparse_array_global_with_duplicates_dedup(
const std::string& array_name);
void check_sparse_array_global_with_all_duplicates_dedup(
const std::string& array_name);
void check_sparse_array_no_results(const std::string& array_name);
void check_non_empty_domain(const std::string& path);
void check_invalid_offsets(const std::string& array_name);
void write_partial_sparse_array(const std::string& array_name);
void write_sparse_array_missing_attributes(const std::string& array_name);
void write_sparse_array(const std::string& array_name);
void write_sparse_array(
const std::string& array_name,
const std::vector<uint64_t>& coords_dim1,
const std::vector<uint64_t>& coords_dim2,
const std::vector<int>& a1,
const std::vector<uint64_t>& a2_off,
const std::vector<char>& a2_val,
const std::vector<float>& a3);
void create_temp_dir(const std::string& path);
void remove_temp_dir(const std::string& path);
static std::string random_name(const std::string& prefix);
void check_sorted_reads(
const std::string& array_name,
tiledb_filter_type_t compressor,
tiledb_layout_t tile_order,
tiledb_layout_t cell_order);
void remove_array(const std::string& array_name);
bool is_array(const std::string& array_name);
/**
* Creates a 2D sparse array.
*
* @param array_name The array name.
* @param tile_extent_0 The tile extent along the first dimension.
* @param tile_extent_1 The tile extent along the second dimension.
* @param domain_0_lo The smallest value of the first dimension domain.
* @param domain_0_hi The largest value of the first dimension domain.
* @param domain_1_lo The smallest value of the second dimension domain.
* @param domain_1_hi The largest value of the second dimension domain.
* @param capacity The tile capacity.
* @param cell_order The cell order.
* @param tile_order The tile order.
*/
void create_sparse_array_2D(
const std::string& array_name,
const int64_t tile_extent_0,
const int64_t tile_extent_1,
const int64_t domain_0_lo,
const int64_t domain_0_hi,
const int64_t domain_1_lo,
const int64_t domain_1_hi,
const uint64_t capacity,
const tiledb_filter_type_t compressor,
const tiledb_layout_t cell_order,
const tiledb_layout_t tile_order);
/**
* Reads a subarray oriented by the input boundaries and outputs the buffer
* containing the attribute values of the corresponding cells.
*
* @param array_name The array name.
* @param domain_0_lo The smallest value of the first dimension domain to
* be read.
* @param domain_0_hi The largest value of the first dimension domain to
* be read.
* @param domain_1_lo The smallest value of the second dimension domain to
* be read.
* @param domain_1_hi The largest value of the second dimension domain to
* be read.
* @param read_mode The read mode.
* @return The buffer with the read values. Note that this function is
* creating the buffer with 'new'. Therefore, make sure to properly delete
* it in the caller. On error, it returns NULL.
*/
int* read_sparse_array_2D(
const std::string& array_name,
const int64_t domain_0_lo,
const int64_t domain_0_hi,
const int64_t domain_1_lo,
const int64_t domain_1_hi,
const tiledb_query_type_t query_type,
const tiledb_layout_t query_layout);
/**
* Write random values in unsorted mode. The buffer is initialized with each
* cell being equalt to row_id*domain_size_1+col_id.
*
* @param array_name The array name.
* @param domain_size_0 The domain size of the first dimension.
* @param domain_size_1 The domain size of the second dimension.
*/
void write_sparse_array_unsorted_2D(
const std::string& array_name,
const int64_t domain_size_0,
const int64_t domain_size_1);
void test_random_subarrays(
const std::string& array_name,
int64_t domain_size_0,
int64_t domain_size_1,
int iter_num);
};
SparseArrayFx::SparseArrayFx()
: fs_vec_(vfs_test_get_fs_vec()) {
// Initialize vfs test
REQUIRE(vfs_test_init(fs_vec_, &ctx_, &vfs_).ok());
std::srand(0);
for (const auto& fs : fs_vec_)
create_temp_dir(fs->temp_dir());
}
SparseArrayFx::~SparseArrayFx() {
for (const auto& fs : fs_vec_)
remove_temp_dir(fs->temp_dir());
// Close vfs test
REQUIRE(vfs_test_close(fs_vec_, ctx_, vfs_).ok());
tiledb_vfs_free(&vfs_);
tiledb_ctx_free(&ctx_);
}
bool SparseArrayFx::is_array(const std::string& array_name) {
tiledb_object_t type = TILEDB_INVALID;
REQUIRE(tiledb_object_type(ctx_, array_name.c_str(), &type) == TILEDB_OK);
return type == TILEDB_ARRAY;
}
void SparseArrayFx::remove_array(const std::string& array_name) {
if (!is_array(array_name))
return;
CHECK(tiledb_object_remove(ctx_, array_name.c_str()) == TILEDB_OK);
}
void SparseArrayFx::create_temp_dir(const std::string& path) {
remove_temp_dir(path);
REQUIRE(tiledb_vfs_create_dir(ctx_, vfs_, path.c_str()) == TILEDB_OK);
}
void SparseArrayFx::remove_temp_dir(const std::string& path) {
int is_dir = 0;
REQUIRE(tiledb_vfs_is_dir(ctx_, vfs_, path.c_str(), &is_dir) == TILEDB_OK);
if (is_dir)
REQUIRE(tiledb_vfs_remove_dir(ctx_, vfs_, path.c_str()) == TILEDB_OK);
}
std::string SparseArrayFx::random_name(const std::string& prefix) {
std::stringstream ss;
ss << prefix << "-" << std::this_thread::get_id() << "-"
<< TILEDB_TIMESTAMP_NOW_MS;
return ss.str();
}
void SparseArrayFx::create_sparse_array_2D(
const std::string& array_name,
const int64_t tile_extent_0,
const int64_t tile_extent_1,
const int64_t domain_0_lo,
const int64_t domain_0_hi,
const int64_t domain_1_lo,
const int64_t domain_1_hi,
const uint64_t capacity,
const tiledb_filter_type_t compressor,
const tiledb_layout_t cell_order,
const tiledb_layout_t tile_order) {
// Prepare and set the array schema object and data structures
int64_t dim_domain[] = {domain_0_lo, domain_0_hi, domain_1_lo, domain_1_hi};
// Create attribute
tiledb_attribute_t* a;
int rc = tiledb_attribute_alloc(ctx_, ATTR_NAME.c_str(), ATTR_TYPE, &a);
REQUIRE(rc == TILEDB_OK);
tiledb_filter_t* filter;
tiledb_filter_list_t* list;
rc = tiledb_filter_alloc(ctx_, compressor, &filter);
CHECK(rc == TILEDB_OK);
if (compressor != TILEDB_FILTER_NONE) {
rc = tiledb_filter_set_option(
ctx_, filter, TILEDB_COMPRESSION_LEVEL, &COMPRESSION_LEVEL);
CHECK(rc == TILEDB_OK);
}
rc = tiledb_filter_list_alloc(ctx_, &list);
CHECK(rc == TILEDB_OK);
rc = tiledb_filter_list_add_filter(ctx_, list, filter);
CHECK(rc == TILEDB_OK);
rc = tiledb_attribute_set_filter_list(ctx_, a, list);
CHECK(rc == TILEDB_OK);
// Create dimensions
tiledb_dimension_t* d1;
rc = tiledb_dimension_alloc(
ctx_, DIM1_NAME, TILEDB_INT64, &dim_domain[0], &tile_extent_0, &d1);
REQUIRE(rc == TILEDB_OK);
tiledb_dimension_t* d2;
rc = tiledb_dimension_alloc(
ctx_, DIM2_NAME, TILEDB_INT64, &dim_domain[2], &tile_extent_1, &d2);
REQUIRE(rc == TILEDB_OK);
// Create domain
tiledb_domain_t* domain;
rc = tiledb_domain_alloc(ctx_, &domain);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_domain_add_dimension(ctx_, domain, d1);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_domain_add_dimension(ctx_, domain, d2);
REQUIRE(rc == TILEDB_OK);
// Create array schema
tiledb_array_schema_t* array_schema;
rc = tiledb_array_schema_alloc(ctx_, ARRAY_TYPE, &array_schema);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_array_schema_set_capacity(ctx_, array_schema, capacity);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_array_schema_set_cell_order(ctx_, array_schema, cell_order);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_array_schema_set_tile_order(ctx_, array_schema, tile_order);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_array_schema_add_attribute(ctx_, array_schema, a);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_array_schema_set_domain(ctx_, array_schema, domain);
REQUIRE(rc == TILEDB_OK);
// Create the array
if (encryption_type != TILEDB_NO_ENCRYPTION) {
tiledb_ctx_free(&ctx_);
tiledb_vfs_free(&vfs_);
tiledb_config_t* config;
tiledb_error_t* error = nullptr;
rc = tiledb_config_alloc(&config, &error);
REQUIRE(rc == TILEDB_OK);
REQUIRE(error == nullptr);
std::string encryption_type_string =
encryption_type_str((tiledb::sm::EncryptionType)encryption_type);
rc = tiledb_config_set(
config, "sm.encryption_type", encryption_type_string.c_str(), &error);
REQUIRE(error == nullptr);
rc = tiledb_config_set(config, "sm.encryption_key", encryption_key, &error);
REQUIRE(rc == TILEDB_OK);
REQUIRE(error == nullptr);
REQUIRE(vfs_test_init(fs_vec_, &ctx_, &vfs_, config).ok());
tiledb_config_free(&config);
}
rc = tiledb_array_create(ctx_, array_name.c_str(), array_schema);
REQUIRE(rc == TILEDB_OK);
// Clean up
tiledb_filter_free(&filter);
tiledb_filter_list_free(&list);
tiledb_attribute_free(&a);
tiledb_dimension_free(&d1);
tiledb_dimension_free(&d2);
tiledb_domain_free(&domain);
tiledb_array_schema_free(&array_schema);
}
int* SparseArrayFx::read_sparse_array_2D(
const std::string& array_name,
const int64_t domain_0_lo,
const int64_t domain_0_hi,
const int64_t domain_1_lo,
const int64_t domain_1_hi,
const tiledb_query_type_t query_type,
const tiledb_layout_t query_layout) {
// Open array
tiledb_array_t* array;
int rc = tiledb_array_alloc(ctx_, array_name.c_str(), &array);
CHECK(rc == TILEDB_OK);
if (encryption_type != TILEDB_NO_ENCRYPTION) {
tiledb_config_t* cfg;
tiledb_error_t* err = nullptr;
rc = tiledb_config_alloc(&cfg, &err);
REQUIRE(rc == TILEDB_OK);
REQUIRE(err == nullptr);
std::string encryption_type_string =
encryption_type_str((tiledb::sm::EncryptionType)encryption_type);
rc = tiledb_config_set(
cfg, "sm.encryption_type", encryption_type_string.c_str(), &err);
REQUIRE(rc == TILEDB_OK);
REQUIRE(err == nullptr);
rc = tiledb_config_set(cfg, "sm.encryption_key", encryption_key, &err);
REQUIRE(rc == TILEDB_OK);
REQUIRE(err == nullptr);
rc = tiledb_array_set_config(ctx_, array, cfg);
REQUIRE(rc == TILEDB_OK);
tiledb_config_free(&cfg);
}
rc = tiledb_array_open(ctx_, array, query_type);
CHECK(rc == TILEDB_OK);
// Prepare the buffers that will store the result
uint64_t buffer_size = 100 * 1024 * 1024;
auto buffer = new int[buffer_size / sizeof(int)];
REQUIRE(buffer != nullptr);
// Create query
tiledb_query_t* query;
rc = tiledb_query_alloc(ctx_, array, query_type, &query);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, ATTR_NAME.c_str(), buffer, &buffer_size);
REQUIRE(rc == TILEDB_OK);
// Set a subarray
int64_t s0[] = {domain_0_lo, domain_0_hi};
int64_t s1[] = {domain_1_lo, domain_1_hi};
rc = tiledb_query_set_layout(ctx_, query, query_layout);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_add_range(ctx_, query, 0, &s0[0], &s0[1], nullptr);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_add_range(ctx_, query, 1, &s1[0], &s1[1], nullptr);
REQUIRE(rc == TILEDB_OK);
// Submit query
rc = tiledb_query_submit(ctx_, query);
REQUIRE(rc == TILEDB_OK);
tiledb_query_status_t status;
rc = tiledb_query_get_status(ctx_, query, &status);
REQUIRE(rc == TILEDB_OK);
REQUIRE(status == TILEDB_COMPLETED);
// Finalize query
rc = tiledb_query_finalize(ctx_, query);
REQUIRE(rc == TILEDB_OK);
// Close array
rc = tiledb_array_close(ctx_, array);
CHECK(rc == TILEDB_OK);
// Clean up
tiledb_array_free(&array);
tiledb_query_free(&query);
// Success - return the created buffer
return buffer;
}
void SparseArrayFx::write_sparse_array(const std::string& array_name) {
// Prepare cell buffers
int buffer_a1[] = {0, 1, 2, 3, 4, 5, 6, 7};
uint64_t buffer_a2[] = {0, 1, 3, 6, 10, 11, 13, 16};
char buffer_var_a2[] = "abbcccddddeffggghhhh";
float buffer_a3[] = {0.1f,
0.2f,
1.1f,
1.2f,
2.1f,
2.2f,
3.1f,
3.2f,
4.1f,
4.2f,
5.1f,
5.2f,
6.1f,
6.2f,
7.1f,
7.2f};
uint64_t buffer_coords_dim1[] = {1, 1, 1, 2, 3, 4, 3, 3};
uint64_t buffer_coords_dim2[] = {1, 2, 4, 3, 1, 2, 3, 4};
void* buffers[] = {buffer_a1,
buffer_a2,
buffer_var_a2,
buffer_a3,
buffer_coords_dim1,
buffer_coords_dim2};
uint64_t buffer_sizes[] = {
sizeof(buffer_a1),
sizeof(buffer_a2),
sizeof(buffer_var_a2) - 1, // No need to store the last '\0' character
sizeof(buffer_a3),
sizeof(buffer_coords_dim1)};
// Open array
tiledb_array_t* array;
int rc = tiledb_array_alloc(ctx_, array_name.c_str(), &array);
CHECK(rc == TILEDB_OK);
rc = tiledb_array_open(ctx_, array, TILEDB_WRITE);
CHECK(rc == TILEDB_OK);
// Create query
tiledb_query_t* query;
const char* attributes[] = {"a1", "a2", "a3", "d1", "d2"};
rc = tiledb_query_alloc(ctx_, array, TILEDB_WRITE, &query);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_layout(ctx_, query, TILEDB_UNORDERED);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[0], buffers[0], &buffer_sizes[0]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[1], buffers[2], &buffer_sizes[2]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_offsets_buffer(
ctx_, query, attributes[1], (uint64_t*)buffers[1], &buffer_sizes[1]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[2], buffers[3], &buffer_sizes[3]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[3], buffers[4], &buffer_sizes[4]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[4], buffers[5], &buffer_sizes[4]);
CHECK(rc == TILEDB_OK);
// Submit query
rc = tiledb_query_submit(ctx_, query);
CHECK(rc == TILEDB_OK);
// Finalize query
rc = tiledb_query_finalize(ctx_, query);
CHECK(rc == TILEDB_OK);
// Close array
rc = tiledb_array_close(ctx_, array);
CHECK(rc == TILEDB_OK);
// Clean up
tiledb_array_free(&array);
tiledb_query_free(&query);
}
void SparseArrayFx::write_sparse_array(
const std::string& array_name,
const std::vector<uint64_t>& coords_dim1,
const std::vector<uint64_t>& coords_dim2,
const std::vector<int>& a1,
const std::vector<uint64_t>& a2_off,
const std::vector<char>& a2_val,
const std::vector<float>& a3) {
const void* buffers[] = {a1.data(),
a2_off.data(),
a2_val.data(),
a3.data(),
coords_dim1.data(),
coords_dim2.data()};
uint64_t buffer_sizes[] = {a1.size() * sizeof(int),
a2_off.size() * sizeof(uint64_t),
a2_val.size() * sizeof(char),
a3.size() * sizeof(float),
coords_dim1.size() * sizeof(uint64_t),
coords_dim2.size() * sizeof(uint64_t)};
// Open array
tiledb_array_t* array;
int rc = tiledb_array_alloc(ctx_, array_name.c_str(), &array);
CHECK(rc == TILEDB_OK);
rc = tiledb_array_open(ctx_, array, TILEDB_WRITE);
CHECK(rc == TILEDB_OK);
// Create query
tiledb_query_t* query;
const char* attributes[] = {"a1", "a2", "a3", "d1", "d2"};
rc = tiledb_query_alloc(ctx_, array, TILEDB_WRITE, &query);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_layout(ctx_, query, TILEDB_UNORDERED);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[0], (void*)buffers[0], &buffer_sizes[0]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[1], (void*)buffers[2], &buffer_sizes[2]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_offsets_buffer(
ctx_, query, attributes[1], (uint64_t*)buffers[1], &buffer_sizes[1]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[2], (void*)buffers[3], &buffer_sizes[3]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[3], (void*)buffers[4], &buffer_sizes[4]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[4], (void*)buffers[5], &buffer_sizes[5]);
CHECK(rc == TILEDB_OK);
// Submit query
rc = tiledb_query_submit(ctx_, query);
CHECK(rc == TILEDB_OK);
// Finalize query
rc = tiledb_query_finalize(ctx_, query);
CHECK(rc == TILEDB_OK);
// Close array
rc = tiledb_array_close(ctx_, array);
CHECK(rc == TILEDB_OK);
// Clean up
tiledb_array_free(&array);
tiledb_query_free(&query);
}
void SparseArrayFx::write_sparse_array_unsorted_2D(
const std::string& array_name,
const int64_t domain_size_0,
const int64_t domain_size_1) {
// Generate random attribute values and coordinates for sparse write
int64_t cell_num = domain_size_0 * domain_size_1;
auto buffer_a1 = new int[cell_num];
auto buffer_coords_dim1 = new int64_t[cell_num];
auto buffer_coords_dim2 = new int64_t[cell_num];
int64_t coords_index = 0L;
for (int64_t i = 0; i < domain_size_0; ++i) {
for (int64_t j = 0; j < domain_size_1; ++j) {
buffer_a1[i * domain_size_1 + j] = i * domain_size_1 + j;
buffer_coords_dim1[coords_index] = i;
buffer_coords_dim2[coords_index] = j;
coords_index++;
}
}
// Prepare buffers
void* buffers[] = {buffer_a1, buffer_coords_dim1, buffer_coords_dim2};
uint64_t buffer_sizes[3];
buffer_sizes[0] = cell_num * sizeof(int);
buffer_sizes[1] = cell_num * sizeof(int64_t);
buffer_sizes[2] = cell_num * sizeof(int64_t);
// Set attributes
const char* attributes[] = {ATTR_NAME.c_str(), DIM1_NAME, DIM2_NAME};
// Open array
tiledb_array_t* array;
int rc = tiledb_array_alloc(ctx_, array_name.c_str(), &array);
CHECK(rc == TILEDB_OK);
if (encryption_type != TILEDB_NO_ENCRYPTION) {
tiledb_config_t* cfg;
tiledb_error_t* err = nullptr;
rc = tiledb_config_alloc(&cfg, &err);
REQUIRE(rc == TILEDB_OK);
REQUIRE(err == nullptr);
std::string encryption_type_string =
encryption_type_str((tiledb::sm::EncryptionType)encryption_type);
rc = tiledb_config_set(
cfg, "sm.encryption_type", encryption_type_string.c_str(), &err);
REQUIRE(rc == TILEDB_OK);
REQUIRE(err == nullptr);
rc = tiledb_config_set(cfg, "sm.encryption_key", encryption_key, &err);
REQUIRE(rc == TILEDB_OK);
REQUIRE(err == nullptr);
rc = tiledb_array_set_config(ctx_, array, cfg);
REQUIRE(rc == TILEDB_OK);
tiledb_config_free(&cfg);
}
rc = tiledb_array_open(ctx_, array, TILEDB_WRITE);
CHECK(rc == TILEDB_OK);
// Create query
tiledb_query_t* query;
rc = tiledb_query_alloc(ctx_, array, TILEDB_WRITE, &query);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[0], buffers[0], &buffer_sizes[0]);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[1], buffers[1], &buffer_sizes[1]);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[2], buffers[2], &buffer_sizes[2]);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_layout(ctx_, query, TILEDB_UNORDERED);
REQUIRE(rc == TILEDB_OK);
// Submit query
rc = tiledb_query_submit(ctx_, query);
REQUIRE(rc == TILEDB_OK);
// Finalize query
rc = tiledb_query_finalize(ctx_, query);
REQUIRE(rc == TILEDB_OK);
// Close array
rc = tiledb_array_close(ctx_, array);
CHECK(rc == TILEDB_OK);
// Clean up
tiledb_array_free(&array);
tiledb_query_free(&query);
// Clean up
delete[] buffer_a1;
delete[] buffer_coords_dim1;
delete[] buffer_coords_dim2;
}
void SparseArrayFx::test_random_subarrays(
const std::string& array_name,
int64_t domain_size_0,
int64_t domain_size_1,
int iter_num) {
// write array_schema_latest cells with value = row id * columns + col id to
// disk
write_sparse_array_unsorted_2D(array_name, domain_size_0, domain_size_1);
// test random subarrays and check with corresponding value set by
// row_id*dim1+col_id. top left corner is always 4,4.
int64_t d0_lo = 4;
int64_t d0_hi = 0;
int64_t d1_lo = 4;
int64_t d1_hi = 0;
int64_t height = 0, width = 0;
for (int iter = 0; iter < iter_num; ++iter) {
height = rand() % (domain_size_0 - d0_lo);
width = rand() % (domain_size_1 - d1_lo);
d0_hi = d0_lo + height;
d1_hi = d1_lo + width;
int64_t index = 0;
// Read subarray
int* buffer = read_sparse_array_2D(
array_name, d0_lo, d0_hi, d1_lo, d1_hi, TILEDB_READ, TILEDB_ROW_MAJOR);
CHECK(buffer != nullptr);
// check
bool allok = true;
for (int64_t i = d0_lo; i <= d0_hi; ++i) {
for (int64_t j = d1_lo; j <= d1_hi; ++j) {
bool match = buffer[index] == i * domain_size_1 + j;
if (!match) {
allok = false;
std::cout << "mismatch: " << i << "," << j << "=" << buffer[index]
<< "!=" << ((i * domain_size_1 + j)) << "\n";
break;
}
++index;
}
if (!allok)
break;
}
// clean up
delete[] buffer;
CHECK(allok);
}
}
void SparseArrayFx::check_sorted_reads(
const std::string& array_name,
tiledb_filter_type_t compressor,
tiledb_layout_t tile_order,
tiledb_layout_t cell_order) {
// Parameters used in this test
int64_t domain_size_0 = 5000;
int64_t domain_size_1 = 1000;
int64_t tile_extent_0 = 100;
int64_t tile_extent_1 = 100;
int64_t domain_0_lo = 0;
int64_t domain_0_hi = domain_size_0 - 1;
int64_t domain_1_lo = 0;
int64_t domain_1_hi = domain_size_1 - 1;
int64_t capacity = 100000;
int iter_num = (compressor != TILEDB_FILTER_BZIP2) ? ITER_NUM : 1;
create_sparse_array_2D(
array_name,
tile_extent_0,
tile_extent_1,
domain_0_lo,
domain_0_hi,
domain_1_lo,
domain_1_hi,
capacity,
compressor,
tile_order,
cell_order);
test_random_subarrays(array_name, domain_size_0, domain_size_1, iter_num);
}
void SparseArrayFx::create_sparse_array(
const std::string& array_name,
tiledb_layout_t layout,
const uint64_t* dim_domain) {
// Create dimensions
uint64_t tile_extents[] = {2, 2};
tiledb_dimension_t* d1;
int rc = tiledb_dimension_alloc(
ctx_, "d1", TILEDB_UINT64, &dim_domain[0], &tile_extents[0], &d1);
CHECK(rc == TILEDB_OK);
tiledb_dimension_t* d2;
rc = tiledb_dimension_alloc(
ctx_, "d2", TILEDB_UINT64, &dim_domain[2], &tile_extents[1], &d2);
CHECK(rc == TILEDB_OK);
// Set up filter list
tiledb_filter_t* filter;
rc = tiledb_filter_alloc(ctx_, TILEDB_FILTER_BZIP2, &filter);
REQUIRE(rc == TILEDB_OK);
int level = 5;
rc = tiledb_filter_set_option(ctx_, filter, TILEDB_COMPRESSION_LEVEL, &level);
REQUIRE(rc == TILEDB_OK);
tiledb_filter_list_t* filter_list;
rc = tiledb_filter_list_alloc(ctx_, &filter_list);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_filter_list_add_filter(ctx_, filter_list, filter);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_dimension_set_filter_list(ctx_, d1, filter_list);
REQUIRE(rc == TILEDB_OK);
// Create domain
tiledb_domain_t* domain;
rc = tiledb_domain_alloc(ctx_, &domain);
CHECK(rc == TILEDB_OK);
rc = tiledb_domain_add_dimension(ctx_, domain, d1);
CHECK(rc == TILEDB_OK);
rc = tiledb_domain_add_dimension(ctx_, domain, d2);
CHECK(rc == TILEDB_OK);
// Create attributes
tiledb_attribute_t* a1;
rc = tiledb_attribute_alloc(ctx_, "a1", TILEDB_INT32, &a1);
CHECK(rc == TILEDB_OK);
rc = set_attribute_compression_filter(ctx_, a1, TILEDB_FILTER_LZ4, -1);
CHECK(rc == TILEDB_OK);
rc = tiledb_attribute_set_cell_val_num(ctx_, a1, 1);
CHECK(rc == TILEDB_OK);
tiledb_attribute_t* a2;
rc = tiledb_attribute_alloc(ctx_, "a2", TILEDB_CHAR, &a2);
CHECK(rc == TILEDB_OK);
rc = set_attribute_compression_filter(ctx_, a2, TILEDB_FILTER_GZIP, -1);
CHECK(rc == TILEDB_OK);
tiledb_attribute_set_cell_val_num(ctx_, a2, TILEDB_VAR_NUM);
tiledb_attribute_t* a3;
rc = tiledb_attribute_alloc(ctx_, "a3", TILEDB_FLOAT32, &a3);
CHECK(rc == TILEDB_OK);
rc = set_attribute_compression_filter(ctx_, a3, TILEDB_FILTER_ZSTD, -1);
CHECK(rc == TILEDB_OK);
rc = tiledb_attribute_set_cell_val_num(ctx_, a3, 2);
CHECK(rc == TILEDB_OK);
// Create array schema
tiledb_array_schema_t* array_schema;
rc = tiledb_array_schema_alloc(ctx_, TILEDB_SPARSE, &array_schema);
CHECK(rc == TILEDB_OK);
rc = tiledb_array_schema_set_cell_order(ctx_, array_schema, layout);
CHECK(rc == TILEDB_OK);
rc = tiledb_array_schema_set_tile_order(ctx_, array_schema, layout);
CHECK(rc == TILEDB_OK);
rc = tiledb_array_schema_set_capacity(ctx_, array_schema, 2);
CHECK(rc == TILEDB_OK);
rc = tiledb_array_schema_set_domain(ctx_, array_schema, domain);
CHECK(rc == TILEDB_OK);
rc = tiledb_array_schema_add_attribute(ctx_, array_schema, a1);
CHECK(rc == TILEDB_OK);
rc = tiledb_array_schema_add_attribute(ctx_, array_schema, a2);
CHECK(rc == TILEDB_OK);
rc = tiledb_array_schema_add_attribute(ctx_, array_schema, a3);
CHECK(rc == TILEDB_OK);
// Check array schema
rc = tiledb_array_schema_check(ctx_, array_schema);
CHECK(rc == TILEDB_OK);
// Create array
rc = tiledb_array_create(ctx_, array_name.c_str(), array_schema);
CHECK(rc == TILEDB_OK);
// Clean up
tiledb_attribute_free(&a1);
tiledb_attribute_free(&a2);
tiledb_attribute_free(&a3);
tiledb_dimension_free(&d1);
tiledb_dimension_free(&d2);
tiledb_filter_free(&filter);
tiledb_filter_list_free(&filter_list);
tiledb_domain_free(&domain);
tiledb_array_schema_free(&array_schema);
}
void SparseArrayFx::check_sparse_array_unordered_with_duplicates_error(
const std::string& array_name) {
// Prepare cell buffers
int buffer_a1[] = {7, 5, 0, 6, 4, 3, 1, 2};
uint64_t buffer_a2[] = {0, 4, 6, 7, 10, 11, 15, 17};
char buffer_a2_var[] = "hhhhffagggeddddbbccc";
float buffer_a3[] = {7.1f,
7.2f,
5.1f,
5.2f,
0.1f,
0.2f,
6.1f,
6.2f,
4.1f,
4.2f,
3.1f,
3.2f,
1.1f,
1.2f,
2.1f,
2.2f};
uint64_t buffer_coords_dim1[] = {3, 4, 1, 3, 3, 2, 1, 1};
uint64_t buffer_coords_dim2[] = {4, 2, 1, 3, 3, 3, 2, 4};
void* buffers[] = {buffer_a1,
buffer_a2,
buffer_a2_var,
buffer_a3,
buffer_coords_dim1,
buffer_coords_dim2};
uint64_t buffer_sizes[] = {sizeof(buffer_a1),
sizeof(buffer_a2),
sizeof(buffer_a2_var) - 1,
sizeof(buffer_a3),
sizeof(buffer_coords_dim1)};
// Open array
tiledb_array_t* array;
int rc = tiledb_array_alloc(ctx_, array_name.c_str(), &array);
CHECK(rc == TILEDB_OK);
rc = tiledb_array_open(ctx_, array, TILEDB_WRITE);
CHECK(rc == TILEDB_OK);
// Create query
tiledb_query_t* query;
const char* attributes[] = {"a1", "a2", "a3", "d1", "d2"};
rc = tiledb_query_alloc(ctx_, array, TILEDB_WRITE, &query);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_layout(ctx_, query, TILEDB_UNORDERED);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[0], buffers[0], &buffer_sizes[0]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[1], buffers[2], &buffer_sizes[2]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_offsets_buffer(
ctx_, query, attributes[1], (uint64_t*)buffers[1], &buffer_sizes[1]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[2], buffers[3], &buffer_sizes[3]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[3], buffers[4], &buffer_sizes[4]);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx_, query, attributes[4], buffers[5], &buffer_sizes[4]);
CHECK(rc == TILEDB_OK);
// Submit query
rc = tiledb_query_submit(ctx_, query);
CHECK(rc == TILEDB_ERR);
// Finalize query
rc = tiledb_query_finalize(ctx_, query);
CHECK(rc == TILEDB_OK);
// Close array
rc = tiledb_array_close(ctx_, array);
CHECK(rc == TILEDB_OK);
// Clean up
tiledb_array_free(&array);
tiledb_query_free(&query);
}
void SparseArrayFx::check_sparse_array_unordered_with_duplicates_no_check(
const std::string& array_name) {
// Create TileDB context with config
tiledb_config_t* config = nullptr;
tiledb_error_t* error = nullptr;
REQUIRE(tiledb_config_alloc(&config, &error) == TILEDB_OK);
REQUIRE(error == nullptr);
REQUIRE(
tiledb_config_set(config, "sm.check_coord_dups", "false", &error) ==
TILEDB_OK);
REQUIRE(error == nullptr);
tiledb_ctx_t* ctx = nullptr;
REQUIRE(tiledb_ctx_alloc(config, &ctx) == TILEDB_OK);
REQUIRE(error == nullptr);
tiledb_config_free(&config);
// Prepare cell buffers
int buffer_a1[] = {7, 5, 0, 6, 4, 3, 1, 2};
uint64_t buffer_a2[] = {0, 4, 6, 7, 10, 11, 15, 17};
char buffer_a2_var[] = "hhhhffagggeddddbbccc";
float buffer_a3[] = {7.1f,
7.2f,
5.1f,
5.2f,
0.1f,
0.2f,
6.1f,
6.2f,
4.1f,
4.2f,
3.1f,
3.2f,
1.1f,
1.2f,
2.1f,
2.2f};
uint64_t buffer_coords_dim1[] = {3, 4, 1, 3, 3, 2, 1, 1};
uint64_t buffer_coords_dim2[] = {4, 2, 1, 3, 3, 3, 2, 4};
void* buffers[] = {buffer_a1,
buffer_a2,