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#ifndef RITSUKO_HDF5_VALIDATE_STRING_HPP
#define RITSUKO_HDF5_VALIDATE_STRING_HPP
#include <string>
#include <vector>
#include <stdexcept>
#include "H5Cpp.h"
#include "get_name.hpp"
#include "get_1d_length.hpp"
#include "get_dimensions.hpp"
#include "pick_1d_block_size.hpp"
#include "pick_nd_block_dimensions.hpp"
#include "IterateNdDataset.hpp"
#include "_strings.hpp"
/**
* @file validate_string.hpp
* @brief Helper functions to validate strings.
*/
namespace ritsuko {
namespace hdf5 {
/**
* Check that a scalar string dataset is valid.
* Currently, this involves checking that there are no `NULL` entries for variable-length string datatypes.
* For fixed-width string datasets, this function is a no-op.
*
* @param handle Handle to the HDF5 string dataset.
*/
inline void validate_scalar_string_dataset(const H5::DataSet& handle) {
auto dtype = handle.getDataType();
if (!dtype.isVariableStr()) {
return;
}
char* vptr;
handle.read(&vptr, dtype);
auto dspace = handle.getSpace(); // don't set as temporary in constructor below, otherwise it gets destroyed and the ID invalidated.
[[maybe_unused]] VariableStringCleaner deletor(dtype.getId(), dspace.getId(), &vptr);
if (vptr == NULL) {
throw std::runtime_error("detected a NULL pointer for a variable length string in '" + get_name(handle) + "'");
}
}
/**
* Check that a 1-dimensional string dataset is valid.
* Currently, this involves checking that there are no `NULL` entries for variable-length string datatypes.
* For fixed-width string datasets, this function is a no-op.
*
* @param handle Handle to the HDF5 string dataset.
* @param full_length Length of the dataset as a 1-dimensional vector.
* @param buffer_size Size of the buffer for holding loaded strings.
*/
inline void validate_1d_string_dataset(const H5::DataSet& handle, hsize_t full_length, hsize_t buffer_size) {
auto dtype = handle.getDataType();
if (!dtype.isVariableStr()) {
return;
}
hsize_t block_size = pick_1d_block_size(handle.getCreatePlist(), full_length, buffer_size);
H5::DataSpace mspace(1, &block_size), dspace(1, &full_length);
std::vector<char*> buffer(block_size);
for (hsize_t i = 0; i < full_length; i += block_size) {
auto available = std::min(full_length - i, block_size);
constexpr hsize_t zero = 0;
mspace.selectHyperslab(H5S_SELECT_SET, &available, &zero);
dspace.selectHyperslab(H5S_SELECT_SET, &available, &i);
handle.read(buffer.data(), dtype, mspace, dspace);
[[maybe_unused]] VariableStringCleaner deletor(dtype.getId(), mspace.getId(), buffer.data());
for (hsize_t j = 0; j < available; ++j) {
if (buffer[j] == NULL) {
throw std::runtime_error("detected a NULL pointer for a variable length string in '" + get_name(handle) + "'");
}
}
}
}
/**
* Overload for `validate_1d_string_dataset()` that automatically determines its length via `get_1d_length()`.
* @param handle Handle to the HDF5 string dataset.
* @param buffer_size Size of the buffer for holding loaded strings.
*/
inline void validate_1d_string_dataset(const H5::DataSet& handle, hsize_t buffer_size) {
validate_1d_string_dataset(handle, get_1d_length(handle, false), buffer_size);
}
/**
* Check that an N-dimensional string dataset is valid.
* Currently, this involves checking that there are no `NULL` entries for variable-length string datatypes.
* For fixed-width string datasets, this function is a no-op.
*
* @param handle Handle to the HDF5 string dataset.
* @param dimensions Dimensions of the dataset.
* @param buffer_size Size of the buffer for holding loaded strings.
*/
inline void validate_nd_string_dataset(const H5::DataSet& handle, const std::vector<hsize_t>& dimensions, hsize_t buffer_size) {
auto stype = handle.getDataType();
if (!stype.isVariableStr()) {
return;
}
auto blocks = pick_nd_block_dimensions(handle.getCreatePlist(), dimensions, buffer_size);
IterateNdDataset iter(dimensions, blocks);
std::vector<char*> buffer;
while (!iter.finished()) {
buffer.resize(iter.current_block_size());
// Scope this to ensure that 'mspace' doesn't get changed by
// 'iter.next()' before the destructor is called.
{
const auto& mspace = iter.memory_space();
[[maybe_unused]] VariableStringCleaner stream(stype.getId(), mspace.getId(), buffer.data());
handle.read(buffer.data(), stype, mspace, iter.file_space());
for (auto x : buffer) {
if (x == NULL) {
throw std::runtime_error("detected NULL pointer in a variable-length string dataset");
}
}
}
iter.next();
}
}
/**
* Overload for `validate_nd_string_dataset()` that automatically determines the dimensions.
* @param handle Handle to the HDF5 string dataset.
* @param buffer_size Size of the buffer for holding loaded strings.
*/
inline void validate_nd_string_dataset(const H5::DataSet& handle, hsize_t buffer_size) {
auto dimensions = get_dimensions(handle, false);
validate_nd_string_dataset(handle, dimensions, buffer_size);
}
/**
* Check that a scalar string attribute is valid.
* Currently, this involves checking that there are no `NULL` entries for variable-length string datatypes.
* For fixed-width string attributes, this function is a no-op.
*
* @param attr Handle to the HDF5 string attribute.
*/
inline void validate_scalar_string_attribute(const H5::Attribute& attr) {
auto dtype = attr.getDataType();
if (!dtype.isVariableStr()) {
return;
}
auto mspace = attr.getSpace();
char* buffer;
attr.read(dtype, &buffer);
[[maybe_unused]] VariableStringCleaner deletor(dtype.getId(), mspace.getId(), &buffer);
if (buffer == NULL) {
throw std::runtime_error("detected a NULL pointer for a variable length string attribute");
}
}
/**
* Check that a 1-dimensional string attribute is valid.
* Currently, this involves checking that there are no `NULL` entries for variable-length string datatypes.
* For fixed-width string attributes, this function is a no-op.
*
* @param attr Handle to the HDF5 string attribute.
* @param full_length Length of the attribute as a 1-dimensional vector.
*/
inline void validate_1d_string_attribute(const H5::Attribute& attr, hsize_t full_length) {
auto dtype = attr.getDataType();
if (!dtype.isVariableStr()) {
return;
}
auto mspace = attr.getSpace();
std::vector<char*> buffer(full_length);
attr.read(dtype, buffer.data());
[[maybe_unused]] VariableStringCleaner deletor(dtype.getId(), mspace.getId(), buffer.data());
for (hsize_t i = 0; i < full_length; ++i) {
if (buffer[i] == NULL) {
throw std::runtime_error("detected a NULL pointer for a variable length string attribute");
}
}
}
/**
* Overload for `validate_1d_string_attribute()` that automatically determines its length via `get_1d_length()`.
* @param attr Handle to the HDF5 string attribute.
*/
inline void validate_1d_string_attribute(const H5::Attribute& attr) {
validate_1d_string_attribute(attr, get_1d_length(attr, false));
}
}
}
#endif
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