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unit-capi-string_dims.cc
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unit-capi-string_dims.cc
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/**
* @file unit-capi-string_dims.cc
*
* @section LICENSE
*
* The MIT License
*
* @copyright Copyright (c) 2017-2021 TileDB Inc.
*
* 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 arrays with string dimensions.
*/
#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/c_api/tiledb_serialization.h"
#include "tiledb/sm/enums/serialization_type.h"
#include "tiledb/sm/misc/utils.h"
#include <chrono>
#include <iostream>
#include <sstream>
#include <thread>
using namespace tiledb::test;
typedef std::pair<std::string, uint64_t> EstSize;
struct StringDimsFx {
/**
* If true, array schema is serialized before submission, to test the
* serialization paths.
*/
bool serialize_ = false;
// TileDB context
tiledb_ctx_t* ctx_;
tiledb_vfs_t* vfs_;
// Vector of supported filsystems
const std::vector<std::unique_ptr<SupportedFs>> fs_vec_;
// Used to get the number of directories or files of another directory
struct get_num_struct {
tiledb_ctx_t* ctx;
tiledb_vfs_t* vfs;
int num;
};
static int get_dir_num(const char* path, void* data);
// Functions
StringDimsFx();
~StringDimsFx();
void create_temp_dir(const std::string& path);
void remove_temp_dir(const std::string& path);
std::string random_name(const std::string& prefix);
int array_create_wrapper(
const std::string& path, tiledb_array_schema_t* array_schema);
int array_schema_load_wrapper(
const std::string& path, tiledb_array_schema_t** array_schema);
void write_array_ascii(const std::string& array_name);
void write_array_1d(
tiledb_ctx_t* ctx,
const std::string& array_name,
tiledb_layout_t layout,
const std::vector<uint64_t>& d_off,
const std::string& d_val,
const std::vector<int32_t>& a);
void write_array_2d(
tiledb_ctx_t* ctx,
const std::string& array_name,
tiledb_layout_t layout,
const std::vector<uint64_t>& d1_off,
const std::string& d1_val,
const std::vector<int32_t>& d2,
const std::vector<int32_t>& a);
int tiledb_array_get_non_empty_domain_var_size_from_name_wrapper(
tiledb_ctx_t* ctx,
tiledb_array_t* array,
const char* name,
uint64_t* start_size,
uint64_t* end_size,
int32_t* is_empty);
int tiledb_array_get_non_empty_domain_var_from_name_wrapper(
tiledb_ctx_t* ctx,
tiledb_array_t* array,
const char* name,
void* start,
void* end,
int32_t* is_empty);
int tiledb_array_get_non_empty_domain_from_name_wrapper(
tiledb_ctx_t* ctx,
tiledb_array_t* array,
const char* name,
void* domain,
int32_t* is_empty);
int tiledb_query_submit_wrapper(
tiledb_ctx_t* ctx, tiledb_query_t* query, const std::string& array_uri);
void get_non_empty_domain(
const std::string& array_name,
const std::string& dim_name,
std::vector<int32_t>* dom,
int32_t* is_empty);
void get_non_empty_domain_var(
const std::string& array_name,
const std::string& dim_name,
std::string* start,
std::string* end,
int32_t* is_empty);
void get_est_result_size_var(
tiledb_array_t* array,
unsigned dim_idx,
const std::string& dim_name,
const std::string& start,
const std::string& end,
uint64_t* size_off,
uint64_t* size_val);
void read_array_1d(
tiledb_ctx_t* ctx,
tiledb_array_t* array,
tiledb_layout_t layout,
const std::string& start,
const std::string& end,
std::vector<uint64_t>* d_off,
std::string* d_val,
std::vector<int32_t>* a,
tiledb_query_status_t* status);
void read_array_2d(
tiledb_ctx_t* ctx,
tiledb_array_t* array,
tiledb_layout_t layout,
const std::string& d1_start,
const std::string& d1_end,
int32_t d2_start,
int32_t d2_end,
std::vector<uint64_t>* d1_off,
std::string* d1_val,
std::vector<int32_t>* d2,
std::vector<int32_t>* a,
tiledb_query_status_t* status);
};
StringDimsFx::StringDimsFx()
: fs_vec_(vfs_test_get_fs_vec()) {
// Initialize vfs test
REQUIRE(vfs_test_init(fs_vec_, &ctx_, &vfs_).ok());
}
StringDimsFx::~StringDimsFx() {
// Close vfs test
REQUIRE(vfs_test_close(fs_vec_, ctx_, vfs_).ok());
tiledb_vfs_free(&vfs_);
tiledb_ctx_free(&ctx_);
}
void StringDimsFx::create_temp_dir(const std::string& path) {
remove_temp_dir(path);
REQUIRE(tiledb_vfs_create_dir(ctx_, vfs_, path.c_str()) == TILEDB_OK);
}
void StringDimsFx::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 StringDimsFx::random_name(const std::string& prefix) {
std::stringstream ss;
ss << prefix << "-" << std::this_thread::get_id() << "-"
<< TILEDB_TIMESTAMP_NOW_MS;
return ss.str();
}
int StringDimsFx::get_dir_num(const char* path, void* data) {
auto data_struct = (StringDimsFx::get_num_struct*)data;
auto ctx = data_struct->ctx;
auto vfs = data_struct->vfs;
int is_dir;
int rc = tiledb_vfs_is_dir(ctx, vfs, path, &is_dir);
CHECK(rc == TILEDB_OK);
auto meta_dir =
std::string("/") + tiledb::sm::constants::array_metadata_folder_name;
auto schema_dir =
std::string("/") + tiledb::sm::constants::array_schema_folder_name;
if (!tiledb::sm::utils::parse::ends_with(path, meta_dir) &&
!tiledb::sm::utils::parse::ends_with(path, schema_dir)) {
// Ignoring the meta folder and the schema folder
data_struct->num += is_dir;
}
return 1;
}
int StringDimsFx::array_schema_load_wrapper(
const std::string& path, tiledb_array_schema_t** array_schema) {
#ifndef TILEDB_SERIALIZATION
return tiledb_array_schema_load(ctx_, path.c_str(), array_schema);
#endif
if (!serialize_) {
return tiledb_array_schema_load(ctx_, path.c_str(), array_schema);
}
// Load array.
int rc = tiledb_array_schema_load(ctx_, path.c_str(), array_schema);
REQUIRE(rc == TILEDB_OK);
// Serialize the array
tiledb_buffer_t* buff;
REQUIRE(
tiledb_serialize_array_schema(
ctx_,
*array_schema,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
1,
&buff) == TILEDB_OK);
// Load array schema from the rest server
tiledb_array_schema_t* new_array_schema = nullptr;
REQUIRE(
tiledb_deserialize_array_schema(
ctx_,
buff,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
0,
&new_array_schema) == TILEDB_OK);
// Serialize the new array schema and deserialize into the original array
// schema.
tiledb_array_schema_free(array_schema);
tiledb_buffer_t* buff2;
REQUIRE(
tiledb_serialize_array_schema(
ctx_,
new_array_schema,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
0,
&buff2) == TILEDB_OK);
REQUIRE(
tiledb_deserialize_array_schema(
ctx_,
buff2,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
1,
array_schema) == TILEDB_OK);
// Clean up.
tiledb_array_schema_free(&new_array_schema);
tiledb_buffer_free(&buff);
tiledb_buffer_free(&buff2);
return rc;
}
int StringDimsFx::array_create_wrapper(
const std::string& path, tiledb_array_schema_t* array_schema) {
#ifndef TILEDB_SERIALIZATION
return tiledb_array_create(ctx_, path.c_str(), array_schema);
#endif
if (!serialize_) {
return tiledb_array_create(ctx_, path.c_str(), array_schema);
}
// Serialize the array
tiledb_buffer_t* buff;
REQUIRE(
tiledb_serialize_array_schema(
ctx_,
array_schema,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
1,
&buff) == TILEDB_OK);
// Load array schema from the rest server
tiledb_array_schema_t* new_array_schema = nullptr;
REQUIRE(
tiledb_deserialize_array_schema(
ctx_,
buff,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
0,
&new_array_schema) == TILEDB_OK);
// Create array from new schema
int rc = tiledb_array_create(ctx_, path.c_str(), new_array_schema);
// Serialize the new array schema and deserialize into the original array
// schema.
tiledb_buffer_t* buff2;
tiledb_array_schema_t* new_array_schema2 = nullptr;
REQUIRE(
tiledb_serialize_array_schema(
ctx_,
new_array_schema,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
0,
&buff2) == TILEDB_OK);
REQUIRE(
tiledb_deserialize_array_schema(
ctx_,
buff2,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
1,
&new_array_schema2) == TILEDB_OK);
// Clean up.
tiledb_array_schema_free(&new_array_schema);
tiledb_array_schema_free(&new_array_schema2);
tiledb_buffer_free(&buff);
tiledb_buffer_free(&buff2);
return rc;
}
int StringDimsFx::tiledb_query_submit_wrapper(
tiledb_ctx_t* ctx, tiledb_query_t* query, const std::string& array_uri) {
#ifndef TILEDB_SERIALIZATION
return tiledb_query_submit(ctx, query);
#endif
if (!serialize_) {
return tiledb_query_submit(ctx, query);
}
// Get the query type and layout
tiledb_query_type_t query_type;
tiledb_layout_t layout;
REQUIRE(tiledb_query_get_type(ctx, query, &query_type) == TILEDB_OK);
REQUIRE(tiledb_query_get_layout(ctx, query, &layout) == TILEDB_OK);
// Serialize the query (client-side).
tiledb_buffer_list_t* buff_list1;
int rc = tiledb_serialize_query(ctx, query, TILEDB_CAPNP, 1, &buff_list1);
// Global order writes are not (yet) supported for serialization. Just
// check that serialization is an error, and then execute the regular query.
if (layout == TILEDB_GLOBAL_ORDER && query_type == TILEDB_WRITE) {
REQUIRE(rc == TILEDB_ERR);
tiledb_buffer_list_free(&buff_list1);
return tiledb_query_submit(ctx, query);
} else {
REQUIRE(rc == TILEDB_OK);
}
// Copy the data to a temporary memory region ("send over the network").
tiledb_buffer_t* buff1;
REQUIRE(tiledb_buffer_list_flatten(ctx, buff_list1, &buff1) == TILEDB_OK);
uint64_t buff1_size;
void* buff1_data;
REQUIRE(
tiledb_buffer_get_data(ctx, buff1, &buff1_data, &buff1_size) ==
TILEDB_OK);
void* buff1_copy = std::malloc(buff1_size);
REQUIRE(buff1_copy != nullptr);
std::memcpy(buff1_copy, buff1_data, buff1_size);
tiledb_buffer_free(&buff1);
// Create a new buffer that wraps the data from the temporary buffer.
// This mimics what the REST server side would do.
tiledb_buffer_t* buff2;
REQUIRE(tiledb_buffer_alloc(ctx, &buff2) == TILEDB_OK);
REQUIRE(
tiledb_buffer_set_data(ctx, buff2, buff1_copy, buff1_size) == TILEDB_OK);
// Open a new array instance.
tiledb_array_t* new_array = nullptr;
REQUIRE(tiledb_array_alloc(ctx, array_uri.c_str(), &new_array) == TILEDB_OK);
REQUIRE(tiledb_array_open(ctx, new_array, query_type) == TILEDB_OK);
// Create a new query and deserialize from the buffer (server-side)
tiledb_query_t* new_query = nullptr;
REQUIRE(
tiledb_query_alloc(ctx, new_array, query_type, &new_query) == TILEDB_OK);
REQUIRE(
tiledb_deserialize_query(ctx, buff2, TILEDB_CAPNP, 0, new_query) ==
TILEDB_OK);
// Next, for reads, allocate buffers for the new query.
std::vector<void*> to_free;
if (query_type == TILEDB_READ) {
tiledb_array_schema_t* schema;
REQUIRE(tiledb_array_get_schema(ctx, new_array, &schema) == TILEDB_OK);
uint32_t num_attributes;
REQUIRE(
tiledb_array_schema_get_attribute_num(ctx, schema, &num_attributes) ==
TILEDB_OK);
for (uint32_t i = 0; i < num_attributes; i++) {
tiledb_attribute_t* attr;
REQUIRE(
tiledb_array_schema_get_attribute_from_index(ctx, schema, i, &attr) ==
TILEDB_OK);
const char* name;
REQUIRE(tiledb_attribute_get_name(ctx, attr, &name) == TILEDB_OK);
uint32_t cell_num;
REQUIRE(
tiledb_attribute_get_cell_val_num(ctx, attr, &cell_num) == TILEDB_OK);
bool var_len = cell_num == TILEDB_VAR_NUM;
if (var_len) {
void* buff;
uint64_t* buff_size;
uint64_t* offset_buff;
uint64_t* offset_buff_size;
REQUIRE(
tiledb_query_get_data_buffer(
ctx, new_query, name, &buff, &buff_size) == TILEDB_OK);
REQUIRE(
tiledb_query_get_offsets_buffer(
ctx, new_query, name, &offset_buff, &offset_buff_size) ==
TILEDB_OK);
// Buffers will always be null after deserialization on server side
REQUIRE(buff == nullptr);
REQUIRE(offset_buff == nullptr);
if (buff_size != nullptr) {
// Buffer size was set for the attribute; allocate one of the
// appropriate size.
buff = std::malloc(*buff_size);
offset_buff = (uint64_t*)std::malloc(*offset_buff_size);
to_free.push_back(buff);
to_free.push_back(offset_buff);
REQUIRE(
tiledb_query_set_data_buffer(
ctx, new_query, name, buff, buff_size) == TILEDB_OK);
REQUIRE(
tiledb_query_set_offsets_buffer(
ctx, new_query, name, offset_buff, offset_buff_size) ==
TILEDB_OK);
}
} else {
void* buff;
uint64_t* buff_size;
REQUIRE(
tiledb_query_get_data_buffer(
ctx, new_query, name, &buff, &buff_size) == TILEDB_OK);
// Buffers will always be null after deserialization on server side
REQUIRE(buff == nullptr);
if (buff_size != nullptr) {
// Buffer size was set for the attribute; allocate one of the
// appropriate size.
buff = std::malloc(*buff_size);
to_free.push_back(buff);
REQUIRE(
tiledb_query_set_data_buffer(
ctx, new_query, name, buff, buff_size) == TILEDB_OK);
}
}
tiledb_attribute_free(&attr);
}
// Repeat for coords
void* buff;
uint64_t* buff_size;
REQUIRE(
tiledb_query_get_data_buffer(
ctx, new_query, TILEDB_COORDS, &buff, &buff_size) == TILEDB_OK);
if (buff_size != nullptr) {
buff = std::malloc(*buff_size);
to_free.push_back(buff);
REQUIRE(
tiledb_query_set_data_buffer(
ctx, new_query, TILEDB_COORDS, buff, buff_size) == TILEDB_OK);
}
// Repeat for split dimensions, if they are set we will set the buffer
uint32_t num_dimension;
tiledb_domain_t* domain;
REQUIRE(tiledb_array_schema_get_domain(ctx, schema, &domain) == TILEDB_OK);
REQUIRE(tiledb_domain_get_ndim(ctx, domain, &num_dimension) == TILEDB_OK);
for (uint32_t i = 0; i < num_dimension; i++) {
tiledb_dimension_t* dim;
REQUIRE(
tiledb_domain_get_dimension_from_index(ctx, domain, i, &dim) ==
TILEDB_OK);
const char* name;
REQUIRE(tiledb_dimension_get_name(ctx, dim, &name) == TILEDB_OK);
void* buff = nullptr;
uint64_t* buff_size = nullptr;
uint64_t* offset_buff = nullptr;
uint64_t* offset_buff_size = nullptr;
uint32_t cell_val_num = 0;
REQUIRE(
tiledb_dimension_get_cell_val_num(ctx, dim, &cell_val_num) ==
TILEDB_OK);
if (cell_val_num == TILEDB_VAR_NUM) {
REQUIRE(
tiledb_query_get_data_buffer(
ctx, new_query, name, &buff, &buff_size) == TILEDB_OK);
REQUIRE(
tiledb_query_get_offsets_buffer(
ctx, new_query, name, &offset_buff, &offset_buff_size) ==
TILEDB_OK);
} else {
REQUIRE(
tiledb_query_get_data_buffer(
ctx, new_query, name, &buff, &buff_size) == TILEDB_OK);
}
// Buffers will always be null after deserialization on server side
REQUIRE(buff == nullptr);
REQUIRE(offset_buff == nullptr);
if (offset_buff_size != nullptr) {
// Buffer size was set for the attribute; allocate one of the
// appropriate size.
offset_buff = static_cast<uint64_t*>(std::malloc(*offset_buff_size));
to_free.push_back(offset_buff);
buff = std::malloc(*buff_size);
to_free.push_back(buff);
REQUIRE(
tiledb_query_set_data_buffer(
ctx, new_query, name, buff, buff_size) == TILEDB_OK);
REQUIRE(
tiledb_query_set_offsets_buffer(
ctx, new_query, name, offset_buff, offset_buff_size) ==
TILEDB_OK);
} else if (buff_size != nullptr) {
// Buffer size was set for the attribute; allocate one of the
// appropriate size.
buff = std::malloc(*buff_size);
to_free.push_back(buff);
REQUIRE(
tiledb_query_set_data_buffer(
ctx, new_query, name, buff, buff_size) == TILEDB_OK);
}
tiledb_dimension_free(&dim);
}
tiledb_domain_free(&domain);
tiledb_array_schema_free(&schema);
}
// Submit the new query ("on the server").
rc = tiledb_query_submit(ctx, new_query);
// Serialize the new query and "send it over the network" (server-side)
tiledb_buffer_list_t* buff_list2;
REQUIRE(
tiledb_serialize_query(ctx, new_query, TILEDB_CAPNP, 0, &buff_list2) ==
TILEDB_OK);
tiledb_buffer_t* buff3;
REQUIRE(tiledb_buffer_list_flatten(ctx, buff_list2, &buff3) == TILEDB_OK);
uint64_t buff3_size;
void* buff3_data;
REQUIRE(
tiledb_buffer_get_data(ctx, buff3, &buff3_data, &buff3_size) ==
TILEDB_OK);
void* buff3_copy = std::malloc(buff3_size);
REQUIRE(buff3_copy != nullptr);
std::memcpy(buff3_copy, buff3_data, buff3_size);
tiledb_buffer_free(&buff2);
tiledb_buffer_free(&buff3);
// Create a new buffer that wraps the data from the temporary buffer.
tiledb_buffer_t* buff4;
REQUIRE(tiledb_buffer_alloc(ctx, &buff4) == TILEDB_OK);
REQUIRE(
tiledb_buffer_set_data(ctx, buff4, buff3_copy, buff3_size) == TILEDB_OK);
// Deserialize into the original query. Client-side
REQUIRE(
tiledb_deserialize_query(ctx, buff4, TILEDB_CAPNP, 1, query) ==
TILEDB_OK);
// Clean up.
REQUIRE(tiledb_array_close(ctx, new_array) == TILEDB_OK);
tiledb_query_free(&new_query);
tiledb_array_free(&new_array);
tiledb_buffer_free(&buff4);
tiledb_buffer_list_free(&buff_list1);
tiledb_buffer_list_free(&buff_list2);
std::free(buff1_copy);
std::free(buff3_copy);
for (void* b : to_free)
std::free(b);
return rc;
}
void StringDimsFx::write_array_ascii(const std::string& array_name) {
// 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 and submit query
tiledb_query_t* query;
rc = tiledb_query_alloc(ctx_, array, TILEDB_WRITE, &query);
REQUIRE(rc == TILEDB_OK);
char d_data[] = "aabbbcdddd";
uint64_t d_data_size = strlen(d_data);
uint64_t d_off[] = {0, 2, 5, 6};
uint64_t d_off_size = sizeof(d_off);
int32_t a_data[] = {1, 2, 3, 4};
uint64_t a_size = sizeof(a_data);
rc = tiledb_query_set_data_buffer(ctx_, query, "d", d_data, &d_data_size);
REQUIRE(rc == TILEDB_ERR);
rc = tiledb_query_set_data_buffer(ctx_, query, "d", d_data, &d_data_size);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_offsets_buffer(ctx_, query, "d", d_off, &d_off_size);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(ctx_, query, "a", a_data, &a_size);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_layout(ctx_, query, TILEDB_GLOBAL_ORDER);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_submit_wrapper(ctx_, query, array_name);
REQUIRE(rc == TILEDB_OK);
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);
}
void StringDimsFx::write_array_1d(
tiledb_ctx_t* ctx,
const std::string& array_name,
tiledb_layout_t layout,
const std::vector<uint64_t>& d_off,
const std::string& d_val,
const std::vector<int32_t>& a) {
// 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 and submit query
tiledb_query_t* query;
rc = tiledb_query_alloc(ctx, array, TILEDB_WRITE, &query);
REQUIRE(rc == TILEDB_OK);
uint64_t d_off_size = d_off.size() * sizeof(uint64_t);
uint64_t d_val_size = d_val.size();
uint64_t a_size = a.size() * sizeof(int32_t);
rc = tiledb_query_set_data_buffer(
ctx, query, "d", (void*)&d_val[0], &d_val_size);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_offsets_buffer(
ctx, query, "d", (uint64_t*)&d_off[0], &d_off_size);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(ctx, query, "a", (void*)a.data(), &a_size);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_layout(ctx, query, layout);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_submit_wrapper(ctx, query, array_name);
REQUIRE(rc == TILEDB_OK);
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);
}
void StringDimsFx::write_array_2d(
tiledb_ctx_t* ctx,
const std::string& array_name,
tiledb_layout_t layout,
const std::vector<uint64_t>& d1_off,
const std::string& d1_val,
const std::vector<int32_t>& d2,
const std::vector<int32_t>& a) {
// 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 and submit query
tiledb_query_t* query;
rc = tiledb_query_alloc(ctx, array, TILEDB_WRITE, &query);
REQUIRE(rc == TILEDB_OK);
uint64_t d1_off_size = d1_off.size() * sizeof(uint64_t);
uint64_t d1_val_size = d1_val.size();
uint64_t d2_size = d2.size() * sizeof(int32_t);
uint64_t a_size = a.size() * sizeof(int32_t);
rc = tiledb_query_set_data_buffer(
ctx, query, "d1", (void*)&d1_val[0], &d1_val_size);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_offsets_buffer(
ctx, query, "d1", (uint64_t*)&d1_off[0], &d1_off_size);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(
ctx, query, "d2", (void*)d2.data(), &d2_size);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_data_buffer(ctx, query, "a", (void*)a.data(), &a_size);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_set_layout(ctx, query, layout);
REQUIRE(rc == TILEDB_OK);
rc = tiledb_query_submit_wrapper(ctx, query, array_name);
REQUIRE(rc == TILEDB_OK);
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);
}
int StringDimsFx::tiledb_array_get_non_empty_domain_from_name_wrapper(
tiledb_ctx_t* ctx,
tiledb_array_t* array,
const char* name,
void* domain,
int32_t* is_empty) {
int ret = tiledb_array_get_non_empty_domain_from_name(
ctx, array, name, domain, is_empty);
#ifndef TILEDB_SERIALIZATION
return ret;
#endif
if (ret != TILEDB_OK || !serialize_)
return ret;
// Serialize the non_empty_domain
tiledb_buffer_t* buff;
REQUIRE(
tiledb_serialize_array_non_empty_domain_all_dimensions(
ctx,
array,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
0,
&buff) == TILEDB_OK);
// Deserialize to validate we can round-trip
REQUIRE(
tiledb_deserialize_array_non_empty_domain_all_dimensions(
ctx,
array,
buff,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
1) == TILEDB_OK);
tiledb_buffer_free(&buff);
return tiledb_array_get_non_empty_domain_from_name(
ctx, array, name, domain, is_empty);
}
void StringDimsFx::get_non_empty_domain(
const std::string& array_name,
const std::string& dim_name,
std::vector<int32_t>* dom,
int32_t* is_empty) {
dom->resize(2);
// 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_READ);
CHECK(rc == TILEDB_OK);
// Get non-empty domain
rc = tiledb_array_get_non_empty_domain_from_name_wrapper(
ctx_, array, dim_name.c_str(), &(*dom)[0], is_empty);
CHECK(rc == TILEDB_OK);
// Close array
rc = tiledb_array_close(ctx_, array);
CHECK(rc == TILEDB_OK);
// Clean up
tiledb_array_free(&array);
}
int StringDimsFx::tiledb_array_get_non_empty_domain_var_size_from_name_wrapper(
tiledb_ctx_t* ctx,
tiledb_array_t* array,
const char* name,
uint64_t* start_size,
uint64_t* end_size,
int32_t* is_empty) {
int ret = tiledb_array_get_non_empty_domain_var_size_from_name(
ctx, array, name, start_size, end_size, is_empty);
#ifndef TILEDB_SERIALIZATION
return ret;
#endif
if (ret != TILEDB_OK || !serialize_)
return ret;
// Serialize the non_empty_domain
tiledb_buffer_t* buff;
REQUIRE(
tiledb_serialize_array_non_empty_domain_all_dimensions(
ctx,
array,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
0,
&buff) == TILEDB_OK);
// Deserialize to validate we can round-trip
REQUIRE(
tiledb_deserialize_array_non_empty_domain_all_dimensions(
ctx,
array,
buff,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
1) == TILEDB_OK);
tiledb_buffer_free(&buff);
return tiledb_array_get_non_empty_domain_var_size_from_name(
ctx, array, name, start_size, end_size, is_empty);
}
int StringDimsFx::tiledb_array_get_non_empty_domain_var_from_name_wrapper(
tiledb_ctx_t* ctx,
tiledb_array_t* array,
const char* name,
void* start,
void* end,
int32_t* is_empty) {
int ret = tiledb_array_get_non_empty_domain_var_from_name(
ctx, array, name, start, end, is_empty);
#ifndef TILEDB_SERIALIZATION
return ret;
#endif
if (ret != TILEDB_OK || !serialize_)
return ret;
// Serialize the non_empty_domain
tiledb_buffer_t* buff;
REQUIRE(
tiledb_serialize_array_non_empty_domain_all_dimensions(
ctx,
array,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
0,
&buff) == TILEDB_OK);
// Deserialize to validate we can round-trip
REQUIRE(
tiledb_deserialize_array_non_empty_domain_all_dimensions(
ctx,
array,
buff,
(tiledb_serialization_type_t)tiledb::sm::SerializationType::CAPNP,
1) == TILEDB_OK);
tiledb_buffer_free(&buff);
return tiledb_array_get_non_empty_domain_var_from_name(
ctx, array, name, start, end, is_empty);
}
void StringDimsFx::get_non_empty_domain_var(
const std::string& array_name,
const std::string& dim_name,
std::string* start,
std::string* end,
int32_t* is_empty) {
// 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_READ);
CHECK(rc == TILEDB_OK);
// Get non-empty domain size
uint64_t start_size = 0, end_size = 0;
rc = tiledb_array_get_non_empty_domain_var_size_from_name_wrapper(
ctx_, array, dim_name.c_str(), &start_size, &end_size, is_empty);
CHECK(rc == TILEDB_OK);
// Get non-empty domain
start->resize(start_size);
end->resize(end_size);
rc = tiledb_array_get_non_empty_domain_var_from_name_wrapper(
ctx_, array, dim_name.c_str(), &(*start)[0], &(*end)[0], is_empty);
CHECK(rc == TILEDB_OK);
// Close array
rc = tiledb_array_close(ctx_, array);
CHECK(rc == TILEDB_OK);
// Clean up
tiledb_array_free(&array);
}
void StringDimsFx::get_est_result_size_var(
tiledb_array_t* array,
unsigned dim_idx,
const std::string& dim_name,
const std::string& start,
const std::string& end,
uint64_t* size_off,
uint64_t* size_val) {
tiledb_query_t* query;
int rc = tiledb_query_alloc(ctx_, array, TILEDB_READ, &query);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_add_range_var(
ctx_, query, dim_idx, start.data(), start.size(), end.data(), end.size());
CHECK(rc == TILEDB_OK);
rc = tiledb_query_get_est_result_size_var(
ctx_, query, dim_name.c_str(), size_off, size_val);
CHECK(rc == TILEDB_OK);
tiledb_query_free(&query);
}
void StringDimsFx::read_array_1d(
tiledb_ctx_t* ctx,
tiledb_array_t* array,
tiledb_layout_t layout,
const std::string& start,
const std::string& end,
std::vector<uint64_t>* d_off,
std::string* d_val,
std::vector<int32_t>* a,
tiledb_query_status_t* status) {
// Create query
tiledb_query_t* query;
int rc = tiledb_query_alloc(ctx, array, TILEDB_READ, &query);
CHECK(rc == TILEDB_OK);
rc = tiledb_query_add_range_var(
ctx, query, 0, start.data(), start.size(), end.data(), end.size());
CHECK(rc == TILEDB_OK);
// Check range num
uint64_t range_num;
rc = tiledb_query_get_range_num(ctx_, query, 0, &range_num);
CHECK(rc == TILEDB_OK);
CHECK(range_num == 1);
// Check getting range from an invalid range index
uint64_t start_size = 0, end_size = 0;
rc = tiledb_query_get_range_var_size(
ctx_, query, 0, 2, &start_size, &end_size);
CHECK(rc == TILEDB_ERR);
std::vector<char> start_data(start_size);
std::vector<char> end_data(end_size);
rc = tiledb_query_get_range_var(
ctx_, query, 0, 2, start_data.data(), end_data.data());
CHECK(rc == TILEDB_ERR);
// Check ranges
rc = tiledb_query_get_range_var_size(
ctx_, query, 0, 0, &start_size, &end_size);
CHECK(rc == TILEDB_OK);
start_data.resize(start_size);
end_data.resize(end_size);
rc = tiledb_query_get_range_var(
ctx_, query, 0, 0, start_data.data(), end_data.data());
CHECK(rc == TILEDB_OK);
CHECK(std::string(start_data.data(), start_data.size()) == start);
CHECK(std::string(end_data.data(), end_data.size()) == end);