/
fragment_metadata.cc
5263 lines (4479 loc) · 169 KB
/
fragment_metadata.cc
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/**
* @file fragment_metadata.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
*
* This file implements the FragmentMetadata class.
*/
#include "tiledb/common/common.h"
#include "tiledb/common/heap_memory.h"
#include "tiledb/common/logger.h"
#include "tiledb/common/memory_tracker.h"
#include "tiledb/sm/array_schema/array_schema.h"
#include "tiledb/sm/array_schema/attribute.h"
#include "tiledb/sm/array_schema/dimension.h"
#include "tiledb/sm/array_schema/domain.h"
#include "tiledb/sm/buffer/buffer.h"
#include "tiledb/sm/filesystem/vfs.h"
#include "tiledb/sm/fragment/fragment_metadata.h"
#include "tiledb/sm/misc/constants.h"
#include "tiledb/sm/misc/parallel_functions.h"
#include "tiledb/sm/misc/utils.h"
#include "tiledb/sm/stats/global_stats.h"
#include "tiledb/sm/storage_manager/storage_manager.h"
#include "tiledb/sm/tile/generic_tile_io.h"
#include "tiledb/sm/tile/tile.h"
#include "tiledb/sm/tile/tile_metadata_generator.h"
#include "tiledb/storage_format/serialization/serializers.h"
#include "tiledb/storage_format/uri/parse_uri.h"
#include "tiledb/type/range/range.h"
#include <cassert>
#include <iostream>
#include <numeric>
#include <string>
using namespace tiledb::common;
using namespace tiledb::type;
namespace tiledb {
namespace sm {
class FragmentMetadataStatusException : public StatusException {
public:
explicit FragmentMetadataStatusException(const std::string& message)
: StatusException("FragmentMetadata", message) {
}
};
/* ****************************** */
/* CONSTRUCTORS & DESTRUCTORS */
/* ****************************** */
FragmentMetadata::FragmentMetadata() {
}
FragmentMetadata::FragmentMetadata(
StorageManager* storage_manager,
MemoryTracker* memory_tracker,
const shared_ptr<const ArraySchema>& array_schema,
const URI& fragment_uri,
const std::pair<uint64_t, uint64_t>& timestamp_range,
bool dense,
bool has_timestamps,
bool has_deletes_meta)
: storage_manager_(storage_manager)
, memory_tracker_(memory_tracker)
, array_schema_(array_schema)
, dense_(dense)
, footer_size_(0)
, footer_offset_(0)
, fragment_uri_(fragment_uri)
, has_consolidated_footer_(false)
, last_tile_cell_num_(0)
, has_timestamps_(has_timestamps)
, has_delete_meta_(has_deletes_meta)
, sparse_tile_num_(0)
, meta_file_size_(0)
, rtree_(RTree(&array_schema_->domain(), constants::rtree_fanout))
, tile_index_base_(0)
, version_(array_schema_->write_version())
, timestamp_range_(timestamp_range)
, array_uri_(array_schema_->array_uri()) {
build_idx_map();
array_schema_name_ = array_schema_->name();
}
FragmentMetadata::~FragmentMetadata() = default;
// Copy initialization
FragmentMetadata::FragmentMetadata(const FragmentMetadata& other) {
storage_manager_ = other.storage_manager_;
array_schema_ = other.array_schema_;
dense_ = other.dense_;
fragment_uri_ = other.fragment_uri_;
timestamp_range_ = other.timestamp_range_;
has_consolidated_footer_ = other.has_consolidated_footer_;
rtree_ = other.rtree_;
meta_file_size_ = other.meta_file_size_;
version_ = other.version_;
tile_index_base_ = other.tile_index_base_;
has_timestamps_ = other.has_timestamps_;
has_delete_meta_ = other.has_delete_meta_;
sparse_tile_num_ = other.sparse_tile_num_;
footer_size_ = other.footer_size_;
footer_offset_ = other.footer_offset_;
idx_map_ = other.idx_map_;
array_schema_name_ = other.array_schema_name_;
array_uri_ = other.array_uri_;
}
FragmentMetadata& FragmentMetadata::operator=(const FragmentMetadata& other) {
storage_manager_ = other.storage_manager_;
array_schema_ = other.array_schema_;
dense_ = other.dense_;
fragment_uri_ = other.fragment_uri_;
timestamp_range_ = other.timestamp_range_;
has_consolidated_footer_ = other.has_consolidated_footer_;
rtree_ = other.rtree_;
meta_file_size_ = other.meta_file_size_;
version_ = other.version_;
tile_index_base_ = other.tile_index_base_;
has_timestamps_ = other.has_timestamps_;
has_delete_meta_ = other.has_delete_meta_;
sparse_tile_num_ = other.sparse_tile_num_;
footer_size_ = other.footer_size_;
footer_offset_ = other.footer_offset_;
idx_map_ = other.idx_map_;
array_schema_name_ = other.array_schema_name_;
array_uri_ = other.array_uri_;
return *this;
}
/* ****************************** */
/* API */
/* ****************************** */
Status FragmentMetadata::set_mbr(uint64_t tile, const NDRange& mbr) {
// For easy reference
tile += tile_index_base_;
RETURN_NOT_OK(rtree_.set_leaf(tile, mbr));
return expand_non_empty_domain(mbr);
}
void FragmentMetadata::set_tile_index_base(uint64_t tile_base) {
tile_index_base_ = tile_base;
}
void FragmentMetadata::set_tile_offset(
const std::string& name, uint64_t tid, uint64_t step) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
assert(tid < tile_offsets_[idx].size());
tile_offsets_[idx][tid] = file_sizes_[idx];
file_sizes_[idx] += step;
}
void FragmentMetadata::set_tile_var_offset(
const std::string& name, uint64_t tid, uint64_t step) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
assert(tid < tile_var_offsets_[idx].size());
tile_var_offsets_[idx][tid] = file_var_sizes_[idx];
file_var_sizes_[idx] += step;
}
void FragmentMetadata::set_tile_var_size(
const std::string& name, uint64_t tid, uint64_t size) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
assert(tid < tile_var_sizes_[idx].size());
tile_var_sizes_[idx][tid] = size;
}
void FragmentMetadata::set_tile_validity_offset(
const std::string& name, uint64_t tid, uint64_t step) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
assert(tid < tile_validity_offsets_[idx].size());
tile_validity_offsets_[idx][tid] = file_validity_sizes_[idx];
file_validity_sizes_[idx] += step;
}
void FragmentMetadata::set_tile_min(
const std::string& name, uint64_t tid, const ByteVec& min) {
const auto size = min.size();
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
auto buff_offset = tid * size;
assert(tid < tile_min_buffer_[idx].size() / size);
memcpy(&tile_min_buffer_[idx][buff_offset], min.data(), size);
}
void FragmentMetadata::set_tile_min_var_size(
const std::string& name, uint64_t tid, uint64_t size) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
auto buff_offset = tid * sizeof(uint64_t);
assert(tid < tile_min_buffer_[idx].size() / sizeof(uint64_t));
auto offset = (uint64_t*)&tile_min_buffer_[idx][buff_offset];
*offset = size;
}
void FragmentMetadata::set_tile_min_var(
const std::string& name, uint64_t tid, const ByteVec& min) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
auto buff_offset = tid * sizeof(uint64_t);
assert(tid < tile_min_buffer_[idx].size() / sizeof(uint64_t));
auto offset = (uint64_t*)&tile_min_buffer_[idx][buff_offset];
auto size = buff_offset != tile_min_buffer_[idx].size() - sizeof(uint64_t) ?
offset[1] - offset[0] :
tile_min_var_buffer_[idx].size() - offset[0];
// Copy var data
if (size) { // avoid (potentially) illegal index ref's when size is zero
memcpy(&tile_min_var_buffer_[idx][offset[0]], min.data(), size);
}
}
void FragmentMetadata::set_tile_max(
const std::string& name, uint64_t tid, const ByteVec& max) {
const auto size = max.size();
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
auto buff_offset = tid * size;
assert(tid < tile_max_buffer_[idx].size() / size);
memcpy(&tile_max_buffer_[idx][buff_offset], max.data(), size);
}
void FragmentMetadata::set_tile_max_var_size(
const std::string& name, uint64_t tid, uint64_t size) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
auto buff_offset = tid * sizeof(uint64_t);
assert(tid < tile_max_buffer_[idx].size() / sizeof(uint64_t));
auto offset = (uint64_t*)&tile_max_buffer_[idx][buff_offset];
*offset = size;
}
void FragmentMetadata::set_tile_max_var(
const std::string& name, uint64_t tid, const ByteVec& max) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
auto buff_offset = tid * sizeof(uint64_t);
assert(tid < tile_max_buffer_[idx].size() / sizeof(uint64_t));
auto offset = (uint64_t*)&tile_max_buffer_[idx][buff_offset];
auto size = buff_offset != tile_max_buffer_[idx].size() - sizeof(uint64_t) ?
offset[1] - offset[0] :
tile_max_var_buffer_[idx].size() - offset[0];
// Copy var data
if (size) { // avoid (potentially) illegal index ref's when size is zero
memcpy(&tile_max_var_buffer_[idx][offset[0]], max.data(), size);
}
}
void FragmentMetadata::convert_tile_min_max_var_sizes_to_offsets(
const std::string& name) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
// Fix the min offsets.
uint64_t offset = tile_min_var_buffer_[idx].size();
auto offsets = (uint64_t*)tile_min_buffer_[idx].data() + tile_index_base_;
for (uint64_t i = tile_index_base_;
i < tile_min_buffer_[idx].size() / sizeof(uint64_t);
i++) {
auto size = *offsets;
*offsets = offset;
offsets++;
offset += size;
}
// Allocate min var data buffer.
tile_min_var_buffer_[idx].resize(offset);
// Fix the max offsets.
offset = tile_max_var_buffer_[idx].size();
offsets = (uint64_t*)tile_max_buffer_[idx].data() + tile_index_base_;
for (uint64_t i = tile_index_base_;
i < tile_max_buffer_[idx].size() / sizeof(uint64_t);
i++) {
auto size = *offsets;
*offsets = offset;
offsets++;
offset += size;
}
// Allocate min var data buffer.
tile_max_var_buffer_[idx].resize(offset);
}
void FragmentMetadata::set_tile_sum(
const std::string& name, uint64_t tid, const ByteVec& sum) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
assert(tid * sizeof(uint64_t) < tile_sums_[idx].size());
memcpy(
&tile_sums_[idx][tid * sizeof(uint64_t)], sum.data(), sizeof(uint64_t));
}
void FragmentMetadata::set_tile_null_count(
const std::string& name, uint64_t tid, uint64_t null_count) {
auto it = idx_map_.find(name);
assert(it != idx_map_.end());
auto idx = it->second;
tid += tile_index_base_;
assert(tid < tile_null_counts_[idx].size());
tile_null_counts_[idx][tid] = null_count;
}
template <>
void FragmentMetadata::compute_fragment_min_max_sum<char>(
const std::string& name);
Status FragmentMetadata::compute_fragment_min_max_sum_null_count() {
std::vector<std::string> names;
names.reserve(idx_map_.size());
for (auto& it : idx_map_) {
names.emplace_back(it.first);
}
// Process all attributes in parallel.
auto status = parallel_for(
storage_manager_->compute_tp(), 0, idx_map_.size(), [&](uint64_t n) {
// For easy reference.
const auto& name = names[n];
const auto& idx = idx_map_[name];
const auto var_size = array_schema_->var_size(name);
const auto type = array_schema_->type(name);
// Compute null count.
fragment_null_counts_[idx] = std::accumulate(
tile_null_counts_[idx].begin(), tile_null_counts_[idx].end(), 0);
if (var_size) {
min_max_var(name);
} else {
// Switch depending on datatype.
switch (type) {
case Datatype::INT8:
compute_fragment_min_max_sum<int8_t>(name);
break;
case Datatype::INT16:
compute_fragment_min_max_sum<int16_t>(name);
break;
case Datatype::INT32:
compute_fragment_min_max_sum<int32_t>(name);
break;
case Datatype::INT64:
compute_fragment_min_max_sum<int64_t>(name);
break;
case Datatype::BOOL:
case Datatype::UINT8:
compute_fragment_min_max_sum<uint8_t>(name);
break;
case Datatype::UINT16:
compute_fragment_min_max_sum<uint16_t>(name);
break;
case Datatype::UINT32:
compute_fragment_min_max_sum<uint32_t>(name);
break;
case Datatype::UINT64:
compute_fragment_min_max_sum<uint64_t>(name);
break;
case Datatype::FLOAT32:
compute_fragment_min_max_sum<float>(name);
break;
case Datatype::FLOAT64:
compute_fragment_min_max_sum<double>(name);
break;
case Datatype::DATETIME_YEAR:
case Datatype::DATETIME_MONTH:
case Datatype::DATETIME_WEEK:
case Datatype::DATETIME_DAY:
case Datatype::DATETIME_HR:
case Datatype::DATETIME_MIN:
case Datatype::DATETIME_SEC:
case Datatype::DATETIME_MS:
case Datatype::DATETIME_US:
case Datatype::DATETIME_NS:
case Datatype::DATETIME_PS:
case Datatype::DATETIME_FS:
case Datatype::DATETIME_AS:
case Datatype::TIME_HR:
case Datatype::TIME_MIN:
case Datatype::TIME_SEC:
case Datatype::TIME_MS:
case Datatype::TIME_US:
case Datatype::TIME_NS:
case Datatype::TIME_PS:
case Datatype::TIME_FS:
case Datatype::TIME_AS:
compute_fragment_min_max_sum<int64_t>(name);
break;
case Datatype::STRING_ASCII:
case Datatype::CHAR:
compute_fragment_min_max_sum<char>(name);
break;
case Datatype::BLOB:
compute_fragment_min_max_sum<std::byte>(name);
break;
default:
break;
}
}
return Status::Ok();
});
RETURN_NOT_OK(status);
return Status::Ok();
}
void FragmentMetadata::set_array_schema(
const shared_ptr<const ArraySchema>& array_schema) {
array_schema_ = array_schema;
// Rebuild index mapping
build_idx_map();
}
uint64_t FragmentMetadata::cell_num() const {
auto tile_num = this->tile_num();
assert(tile_num != 0);
if (dense_) { // Dense fragment
return tile_num * array_schema_->domain().cell_num_per_tile();
} else { // Sparse fragment
return (tile_num - 1) * array_schema_->capacity() + last_tile_cell_num();
}
}
uint64_t FragmentMetadata::cell_num(uint64_t tile_pos) const {
if (dense_)
return array_schema_->domain().cell_num_per_tile();
uint64_t tile_num = this->tile_num();
if (tile_pos != tile_num - 1)
return array_schema_->capacity();
return last_tile_cell_num();
}
std::vector<Datatype> FragmentMetadata::dim_types() const {
std::vector<Datatype> ret;
for (uint32_t d = 0; d < array_schema_->dim_num(); d++) {
ret.emplace_back(array_schema_->dimension_ptr(d)->type());
}
return ret;
}
Status FragmentMetadata::add_max_buffer_sizes(
const EncryptionKey& encryption_key,
const void* subarray,
std::unordered_map<std::string, std::pair<uint64_t, uint64_t>>*
buffer_sizes) {
// Dense case
if (dense_)
return add_max_buffer_sizes_dense(subarray, buffer_sizes);
// Convert subarray to NDRange
auto dim_num = array_schema_->dim_num();
auto sub_ptr = (const unsigned char*)subarray;
NDRange sub_nd(dim_num);
uint64_t offset = 0;
for (unsigned d = 0; d < dim_num; ++d) {
auto r_size{2 * array_schema_->dimension_ptr(d)->coord_size()};
sub_nd[d].set_range(&sub_ptr[offset], r_size);
offset += r_size;
}
// Sparse case
return add_max_buffer_sizes_sparse(encryption_key, sub_nd, buffer_sizes);
}
Status FragmentMetadata::add_max_buffer_sizes_dense(
const void* subarray,
std::unordered_map<std::string, std::pair<uint64_t, uint64_t>>*
buffer_sizes) {
// Note: applicable only to the dense case where all dimensions
// have the same type
auto type{array_schema_->dimension_ptr(0)->type()};
switch (type) {
case Datatype::INT32:
return add_max_buffer_sizes_dense<int32_t>(
static_cast<const int32_t*>(subarray), buffer_sizes);
case Datatype::INT64:
return add_max_buffer_sizes_dense<int64_t>(
static_cast<const int64_t*>(subarray), buffer_sizes);
case Datatype::FLOAT32:
return add_max_buffer_sizes_dense<float>(
static_cast<const float*>(subarray), buffer_sizes);
case Datatype::FLOAT64:
return add_max_buffer_sizes_dense<double>(
static_cast<const double*>(subarray), buffer_sizes);
case Datatype::INT8:
return add_max_buffer_sizes_dense<int8_t>(
static_cast<const int8_t*>(subarray), buffer_sizes);
case Datatype::UINT8:
return add_max_buffer_sizes_dense<uint8_t>(
static_cast<const uint8_t*>(subarray), buffer_sizes);
case Datatype::INT16:
return add_max_buffer_sizes_dense<int16_t>(
static_cast<const int16_t*>(subarray), buffer_sizes);
case Datatype::UINT16:
return add_max_buffer_sizes_dense<uint16_t>(
static_cast<const uint16_t*>(subarray), buffer_sizes);
case Datatype::UINT32:
return add_max_buffer_sizes_dense<uint32_t>(
static_cast<const uint32_t*>(subarray), buffer_sizes);
case Datatype::UINT64:
return add_max_buffer_sizes_dense<uint64_t>(
static_cast<const uint64_t*>(subarray), buffer_sizes);
case Datatype::DATETIME_YEAR:
case Datatype::DATETIME_MONTH:
case Datatype::DATETIME_WEEK:
case Datatype::DATETIME_DAY:
case Datatype::DATETIME_HR:
case Datatype::DATETIME_MIN:
case Datatype::DATETIME_SEC:
case Datatype::DATETIME_MS:
case Datatype::DATETIME_US:
case Datatype::DATETIME_NS:
case Datatype::DATETIME_PS:
case Datatype::DATETIME_FS:
case Datatype::DATETIME_AS:
case Datatype::TIME_HR:
case Datatype::TIME_MIN:
case Datatype::TIME_SEC:
case Datatype::TIME_MS:
case Datatype::TIME_US:
case Datatype::TIME_NS:
case Datatype::TIME_PS:
case Datatype::TIME_FS:
case Datatype::TIME_AS:
return add_max_buffer_sizes_dense<int64_t>(
static_cast<const int64_t*>(subarray), buffer_sizes);
default:
return LOG_STATUS(Status_FragmentMetadataError(
"Cannot compute add read buffer sizes for dense array; Unsupported "
"domain type"));
}
return Status::Ok();
}
template <class T>
Status FragmentMetadata::add_max_buffer_sizes_dense(
const T* subarray,
std::unordered_map<std::string, std::pair<uint64_t, uint64_t>>*
buffer_sizes) {
// Calculate the ids of all tiles overlapping with subarray
auto tids = compute_overlapping_tile_ids(subarray);
// Compute buffer sizes
for (auto& tid : tids) {
for (auto& it : *buffer_sizes) {
if (array_schema_->var_size(it.first)) {
auto cell_num = this->cell_num(tid);
it.second.first += cell_num * constants::cell_var_offset_size;
auto&& [st, size] = tile_var_size(it.first, tid);
RETURN_NOT_OK(st);
it.second.second += *size;
} else {
it.second.first += cell_num(tid) * array_schema_->cell_size(it.first);
}
}
}
return Status::Ok();
}
Status FragmentMetadata::add_max_buffer_sizes_sparse(
const EncryptionKey& encryption_key,
const NDRange& subarray,
std::unordered_map<std::string, std::pair<uint64_t, uint64_t>>*
buffer_sizes) {
RETURN_NOT_OK(load_rtree(encryption_key));
// Get tile overlap
std::vector<bool> is_default(subarray.size(), false);
auto tile_overlap = rtree_.get_tile_overlap(subarray, is_default);
// Handle tile ranges
for (const auto& tr : tile_overlap.tile_ranges_) {
for (uint64_t tid = tr.first; tid <= tr.second; ++tid) {
for (auto& it : *buffer_sizes) {
if (array_schema_->var_size(it.first)) {
auto cell_num = this->cell_num(tid);
it.second.first += cell_num * constants::cell_var_offset_size;
auto&& [st, size] = tile_var_size(it.first, tid);
RETURN_NOT_OK(st);
it.second.second += *size;
} else {
it.second.first += cell_num(tid) * array_schema_->cell_size(it.first);
}
}
}
}
// Handle individual tiles
for (const auto& t : tile_overlap.tiles_) {
auto tid = t.first;
for (auto& it : *buffer_sizes) {
if (array_schema_->var_size(it.first)) {
auto cell_num = this->cell_num(tid);
it.second.first += cell_num * constants::cell_var_offset_size;
auto&& [st, size] = tile_var_size(it.first, tid);
it.second.second += *size;
RETURN_NOT_OK(st);
} else {
it.second.first += cell_num(tid) * array_schema_->cell_size(it.first);
}
}
}
return Status::Ok();
}
bool FragmentMetadata::dense() const {
return dense_;
}
const NDRange& FragmentMetadata::domain() const {
return domain_;
}
uint32_t FragmentMetadata::format_version() const {
return version_;
}
Status FragmentMetadata::fragment_size(uint64_t* size) const {
// Add file sizes
*size = 0;
for (const auto& file_size : file_sizes_)
*size += file_size;
for (const auto& file_var_size : file_var_sizes_)
*size += file_var_size;
for (const auto& file_validity_size : file_validity_sizes_)
*size += file_validity_size;
// The fragment metadata file size can be empty when we've loaded consolidated
// metadata
uint64_t meta_file_size = meta_file_size_;
if (meta_file_size == 0) {
auto meta_uri = fragment_uri_.join_path(
std::string(constants::fragment_metadata_filename));
RETURN_NOT_OK(
storage_manager_->vfs()->file_size(meta_uri, &meta_file_size));
}
// Validate that the meta_file_size is not zero, either preloaded or fetched
// above
assert(meta_file_size != 0);
// Add fragment metadata file size
*size += meta_file_size;
return Status::Ok();
}
const URI& FragmentMetadata::fragment_uri() const {
return fragment_uri_;
}
bool FragmentMetadata::has_consolidated_footer() const {
return has_consolidated_footer_;
}
Status FragmentMetadata::get_tile_overlap(
const NDRange& range,
std::vector<bool>& is_default,
TileOverlap* tile_overlap) {
assert(version_ <= 2 || loaded_metadata_.rtree_);
*tile_overlap = rtree_.get_tile_overlap(range, is_default);
return Status::Ok();
}
void FragmentMetadata::compute_tile_bitmap(
const Range& range, unsigned d, std::vector<uint8_t>* tile_bitmap) {
assert(version_ <= 2 || loaded_metadata_.rtree_);
rtree_.compute_tile_bitmap(range, d, tile_bitmap);
}
Status FragmentMetadata::init(const NDRange& non_empty_domain) {
// For easy reference
auto num = num_dims_and_attrs();
auto& domain{array_schema_->domain()};
// Sanity check
assert(!non_empty_domain.empty());
assert(non_empty_domain_.empty());
assert(domain_.empty());
// Set non-empty domain for dense arrays (for sparse it will be calculated
// via the MBRs)
if (dense_) {
non_empty_domain_ = non_empty_domain;
// The following is needed in case the fragment is a result of
// dense consolidation, as the consolidator may have expanded
// the fragment domain beyond the array domain to include
// integral space tiles
domain.crop_ndrange(&non_empty_domain_);
// Set expanded domain
domain_ = non_empty_domain_;
domain.expand_to_tiles(&domain_);
}
// Set last tile cell number
last_tile_cell_num_ = 0;
// Initialize tile offsets
tile_offsets_.resize(num);
tile_offsets_mtx_.resize(num);
file_sizes_.resize(num);
for (unsigned int i = 0; i < num; ++i)
file_sizes_[i] = 0;
// Initialize variable tile offsets
tile_var_offsets_.resize(num);
tile_var_offsets_mtx_.resize(num);
file_var_sizes_.resize(num);
for (unsigned int i = 0; i < num; ++i)
file_var_sizes_[i] = 0;
// Initialize variable tile sizes
tile_var_sizes_.resize(num);
// Initialize validity tile offsets
tile_validity_offsets_.resize(num);
file_validity_sizes_.resize(num);
for (unsigned int i = 0; i < num; ++i)
file_validity_sizes_[i] = 0;
// Initialize tile min/max/sum/null count
tile_min_buffer_.resize(num);
tile_min_var_buffer_.resize(num);
tile_max_buffer_.resize(num);
tile_max_var_buffer_.resize(num);
tile_sums_.resize(num);
tile_null_counts_.resize(num);
// Initialize fragment min/max/sum/null count
fragment_mins_.resize(num);
fragment_maxs_.resize(num);
fragment_sums_.resize(num);
fragment_null_counts_.resize(num);
return Status::Ok();
}
uint64_t FragmentMetadata::last_tile_cell_num() const {
return last_tile_cell_num_;
}
Status FragmentMetadata::load(
const EncryptionKey& encryption_key,
Buffer* f_buff,
uint64_t offset,
std::unordered_map<std::string, shared_ptr<ArraySchema>> array_schemas) {
auto meta_uri = fragment_uri_.join_path(
std::string(constants::fragment_metadata_filename));
// Load the metadata file size when we are not reading from consolidated
// buffer
if (f_buff == nullptr)
RETURN_NOT_OK(
storage_manager_->vfs()->file_size(meta_uri, &meta_file_size_));
// Get fragment name version
uint32_t f_version;
auto name = fragment_uri_.remove_trailing_slash().last_path_part();
RETURN_NOT_OK(utils::parse::get_fragment_name_version(name, &f_version));
// Note: The fragment name version is different from the fragment format
// version.
// - Version 1 corresponds to format versions 1 and 2
// * __uuid_<t1>{_t2}
// - Version 2 corresponds to version 3 and 4
// * __t1_t2_uuid
// - Version 3 corresponds to version 5 or higher
// * __t1_t2_uuid_version
if (f_version == 1)
return load_v1_v2(encryption_key, array_schemas);
return load_v3_or_higher(encryption_key, f_buff, offset, array_schemas);
}
Status FragmentMetadata::store(const EncryptionKey& encryption_key) {
auto timer_se =
storage_manager_->stats()->start_timer("write_store_frag_meta");
assert(version_ >= 7);
if (version_ <= 10) {
return store_v7_v10(encryption_key);
} else if (version_ == 11) {
return store_v11(encryption_key);
} else if (version_ <= 14) {
return store_v12_v14(encryption_key);
} else {
return store_v15_or_higher(encryption_key);
}
assert(false);
return Status::Ok();
}
Status FragmentMetadata::store_v7_v10(const EncryptionKey& encryption_key) {
auto fragment_metadata_uri =
fragment_uri_.join_path(constants::fragment_metadata_filename);
auto num = num_dims_and_attrs();
uint64_t offset = 0, nbytes;
// Store R-Tree
gt_offsets_.rtree_ = offset;
RETURN_NOT_OK_ELSE(store_rtree(encryption_key, &nbytes), clean_up());
offset += nbytes;
// Store tile offsets
gt_offsets_.tile_offsets_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_offsets_[i] = offset;
RETURN_NOT_OK_ELSE(
store_tile_offsets(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store tile var offsets
gt_offsets_.tile_var_offsets_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_var_offsets_[i] = offset;
RETURN_NOT_OK_ELSE(
store_tile_var_offsets(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store tile var sizes
gt_offsets_.tile_var_sizes_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_var_sizes_[i] = offset;
RETURN_NOT_OK_ELSE(
store_tile_var_sizes(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store validity tile offsets
gt_offsets_.tile_validity_offsets_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_validity_offsets_[i] = offset;
RETURN_NOT_OK_ELSE(
store_tile_validity_offsets(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store footer
RETURN_NOT_OK_ELSE(store_footer(encryption_key), clean_up());
// Close file
return storage_manager_->close_file(fragment_metadata_uri);
}
Status FragmentMetadata::store_v11(const EncryptionKey& encryption_key) {
auto fragment_metadata_uri =
fragment_uri_.join_path(constants::fragment_metadata_filename);
auto num = num_dims_and_attrs();
uint64_t offset = 0, nbytes;
// Store R-Tree
gt_offsets_.rtree_ = offset;
RETURN_NOT_OK_ELSE(store_rtree(encryption_key, &nbytes), clean_up());
offset += nbytes;
// Store tile offsets
gt_offsets_.tile_offsets_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_offsets_[i] = offset;
RETURN_NOT_OK_ELSE(
store_tile_offsets(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store tile var offsets
gt_offsets_.tile_var_offsets_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_var_offsets_[i] = offset;
RETURN_NOT_OK_ELSE(
store_tile_var_offsets(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store tile var sizes
gt_offsets_.tile_var_sizes_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_var_sizes_[i] = offset;
RETURN_NOT_OK_ELSE(
store_tile_var_sizes(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store validity tile offsets
gt_offsets_.tile_validity_offsets_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_validity_offsets_[i] = offset;
RETURN_NOT_OK_ELSE(
store_tile_validity_offsets(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store mins
gt_offsets_.tile_min_offsets_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_min_offsets_[i] = offset;
RETURN_NOT_OK_ELSE(store_tile_mins(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store maxs
gt_offsets_.tile_max_offsets_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_max_offsets_[i] = offset;
RETURN_NOT_OK_ELSE(store_tile_maxs(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store sums
gt_offsets_.tile_sum_offsets_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_sum_offsets_[i] = offset;
RETURN_NOT_OK_ELSE(store_tile_sums(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store null counts
gt_offsets_.tile_null_count_offsets_.resize(num);
for (unsigned int i = 0; i < num; ++i) {
gt_offsets_.tile_null_count_offsets_[i] = offset;
RETURN_NOT_OK_ELSE(
store_tile_null_counts(i, encryption_key, &nbytes), clean_up());
offset += nbytes;
}
// Store footer
RETURN_NOT_OK_ELSE(store_footer(encryption_key), clean_up());
// Close file