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Wrap all used H5{L,G} functions. #888

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Dec 8, 2023
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Wrap all used H5{L,G} functions. #888

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170 changes: 69 additions & 101 deletions include/highfive/bits/H5Node_traits_misc.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,6 @@

#include <H5Apublic.h>
#include <H5Fpublic.h>
#include <H5Gpublic.h>
#include <H5Ppublic.h>
#include <H5Tpublic.h>

Expand All @@ -26,6 +25,10 @@
#include "H5Selection_misc.hpp"
#include "H5Slice_traits_misc.hpp"

#include "h5l_wrapper.hpp"
#include "h5g_wrapper.hpp"


namespace HighFive {


Expand Down Expand Up @@ -122,16 +125,11 @@
inline Group NodeTraits<Derivate>::createGroup(const std::string& group_name, bool parents) {
LinkCreateProps lcpl;
lcpl.add(CreateIntermediateGroup(parents));
const auto hid = H5Gcreate2(static_cast<Derivate*>(this)->getId(),
group_name.c_str(),
lcpl.getId(),
H5P_DEFAULT,
H5P_DEFAULT);
if (hid < 0) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to create the group \"") +
group_name + "\":");
}
return detail::make_group(hid);
return detail::make_group(detail::h5g_create2(static_cast<Derivate*>(this)->getId(),
group_name.c_str(),
lcpl.getId(),
H5P_DEFAULT,
H5P_DEFAULT));
}

template <typename Derivate>
Expand All @@ -140,27 +138,18 @@
bool parents) {
LinkCreateProps lcpl;
lcpl.add(CreateIntermediateGroup(parents));
const auto hid = H5Gcreate2(static_cast<Derivate*>(this)->getId(),
group_name.c_str(),
lcpl.getId(),
createProps.getId(),
H5P_DEFAULT);
if (hid < 0) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to create the group \"") +
group_name + "\":");
}
return detail::make_group(hid);
return detail::make_group(detail::h5g_create2(static_cast<Derivate*>(this)->getId(),
group_name.c_str(),
lcpl.getId(),
createProps.getId(),
H5P_DEFAULT));
}

template <typename Derivate>
inline Group NodeTraits<Derivate>::getGroup(const std::string& group_name) const {
const auto hid =
H5Gopen2(static_cast<const Derivate*>(this)->getId(), group_name.c_str(), H5P_DEFAULT);
if (hid < 0) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to open the group \"") +
group_name + "\":");
}
return detail::make_group(hid);
return detail::make_group(detail::h5g_open2(static_cast<const Derivate*>(this)->getId(),
group_name.c_str(),
H5P_DEFAULT));
}

template <typename Derivate>
Expand All @@ -174,24 +163,21 @@
template <typename Derivate>
inline size_t NodeTraits<Derivate>::getNumberObjects() const {
hsize_t res;
if (H5Gget_num_objs(static_cast<const Derivate*>(this)->getId(), &res) < 0) {
HDF5ErrMapper::ToException<GroupException>(
std::string("Unable to count objects in existing group or file"));
}
detail::h5g_get_num_objs(static_cast<const Derivate*>(this)->getId(), &res);
return static_cast<size_t>(res);
}

template <typename Derivate>
inline std::string NodeTraits<Derivate>::getObjectName(size_t index) const {
return details::get_name([&](char* buffer, size_t length) {
return H5Lget_name_by_idx(static_cast<const Derivate*>(this)->getId(),
".",
H5_INDEX_NAME,
H5_ITER_INC,
index,
buffer,
length,
H5P_DEFAULT);
return detail::h5l_get_name_by_idx(static_cast<const Derivate*>(this)->getId(),
".",
H5_INDEX_NAME,
H5_ITER_INC,
index,
buffer,
length,
H5P_DEFAULT);
});
}

Expand All @@ -201,18 +187,14 @@
bool parents) const {
LinkCreateProps lcpl;
lcpl.add(CreateIntermediateGroup(parents));
herr_t status = H5Lmove(static_cast<const Derivate*>(this)->getId(),
src_path.c_str(),
static_cast<const Derivate*>(this)->getId(),
dst_path.c_str(),
lcpl.getId(),
H5P_DEFAULT);
if (status < 0) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to move link to \"") +
dst_path + "\":");
return false;
}
return true;
herr_t err = detail::h5l_move(static_cast<const Derivate*>(this)->getId(),
src_path.c_str(),
static_cast<const Derivate*>(this)->getId(),
dst_path.c_str(),
lcpl.getId(),
H5P_DEFAULT);

return err >= 0;
}

template <typename Derivate>
Expand All @@ -223,23 +205,21 @@
size_t num_objs = getNumberObjects();
names.reserve(num_objs);

if (H5Literate(static_cast<const Derivate*>(this)->getId(),
static_cast<H5_index_t>(idx_type),
H5_ITER_INC,
NULL,
&details::internal_high_five_iterate<H5L_info_t>,
static_cast<void*>(&iterateData)) < 0) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to list objects in group"));
}

detail::h5l_iterate(static_cast<const Derivate*>(this)->getId(),
static_cast<H5_index_t>(idx_type),
H5_ITER_INC,
NULL,
&details::internal_high_five_iterate<H5L_info_t>,
static_cast<void*>(&iterateData));
return names;
}

template <typename Derivate>
inline bool NodeTraits<Derivate>::_exist(const std::string& node_name, bool raise_errors) const {
SilenceHDF5 silencer{};
const auto val =
H5Lexists(static_cast<const Derivate*>(this)->getId(), node_name.c_str(), H5P_DEFAULT);
const auto val = detail::nothrow::h5l_exists(static_cast<const Derivate*>(this)->getId(),
node_name.c_str(),
H5P_DEFAULT);
if (val < 0) {
if (raise_errors) {
HDF5ErrMapper::ToException<GroupException>("Invalid link for exist()");
Expand Down Expand Up @@ -269,11 +249,7 @@

template <typename Derivate>
inline void NodeTraits<Derivate>::unlink(const std::string& node_name) const {
const herr_t val =
H5Ldelete(static_cast<const Derivate*>(this)->getId(), node_name.c_str(), H5P_DEFAULT);
if (val < 0) {
HDF5ErrMapper::ToException<GroupException>(std::string("Invalid name for unlink() "));
}
detail::h5l_delete(static_cast<const Derivate*>(this)->getId(), node_name.c_str(), H5P_DEFAULT);
}


Expand All @@ -297,13 +273,14 @@
template <typename Derivate>
inline LinkType NodeTraits<Derivate>::getLinkType(const std::string& node_name) const {
H5L_info_t linkinfo;
if (H5Lget_info(static_cast<const Derivate*>(this)->getId(),
node_name.c_str(),
&linkinfo,
H5P_DEFAULT) < 0 ||
linkinfo.type == H5L_TYPE_ERROR) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to obtain info for link ") +
node_name);
detail::h5l_get_info(static_cast<const Derivate*>(this)->getId(),
node_name.c_str(),
&linkinfo,
H5P_DEFAULT);

if (linkinfo.type == H5L_TYPE_ERROR) {
HDF5ErrMapper::ToException<GroupException>(std::string("Link type of \"") + node_name +

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"\" is H5L_TYPE_ERROR");
}
return _convert_link_type(linkinfo.type);
}
Expand All @@ -323,14 +300,11 @@
if (parents) {
linkCreateProps.add(CreateIntermediateGroup{});
}
auto status = H5Lcreate_soft(obj_path.c_str(),
static_cast<const Derivate*>(this)->getId(),
link_name.c_str(),
linkCreateProps.getId(),
linkAccessProps.getId());
if (status < 0) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to create soft link: "));
}
detail::h5l_create_soft(obj_path.c_str(),
static_cast<const Derivate*>(this)->getId(),
link_name.c_str(),
linkCreateProps.getId(),
linkAccessProps.getId());
}


Expand All @@ -344,15 +318,12 @@
if (parents) {
linkCreateProps.add(CreateIntermediateGroup{});
}
auto status = H5Lcreate_external(h5_file.c_str(),
obj_path.c_str(),
static_cast<const Derivate*>(this)->getId(),
link_name.c_str(),
linkCreateProps.getId(),
linkAccessProps.getId());
if (status < 0) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to create external link: "));
}
detail::h5l_create_external(h5_file.c_str(),
obj_path.c_str(),
static_cast<const Derivate*>(this)->getId(),
link_name.c_str(),
linkCreateProps.getId(),
linkAccessProps.getId());
}

template <typename Derivate>
Expand All @@ -367,15 +338,12 @@
if (parents) {
linkCreateProps.add(CreateIntermediateGroup{});
}
auto status = H5Lcreate_hard(target_obj.getId(),
".",
static_cast<const Derivate*>(this)->getId(),
link_name.c_str(),
linkCreateProps.getId(),
linkAccessProps.getId());
if (status < 0) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to create hard link: "));
}
detail::h5l_create_hard(target_obj.getId(),
".",
static_cast<const Derivate*>(this)->getId(),
link_name.c_str(),
linkCreateProps.getId(),
linkAccessProps.getId());
}


Expand Down
46 changes: 46 additions & 0 deletions include/highfive/bits/h5g_wrapper.hpp
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Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
#pragma once

#include <H5Dpublic.h>
#include <H5Ipublic.h>

#include <highfive/H5Exception.hpp>

namespace HighFive {
namespace detail {

inline hid_t h5g_create2(hid_t loc_id,
const char* name,
hid_t lcpl_id,
hid_t gcpl_id,
hid_t gapl_id) {
hid_t group_id = H5Gcreate2(loc_id, name, lcpl_id, gcpl_id, gapl_id);
if (group_id == H5I_INVALID_HID) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to create the group \"") +
name + "\":");
}

return group_id;
}

inline hid_t h5g_open2(hid_t loc_id, const char* name, hid_t gapl_id) {
hid_t group_id = H5Gopen2(loc_id, name, gapl_id);
if (group_id == H5I_INVALID_HID) {
HDF5ErrMapper::ToException<GroupException>(std::string("Unable to open the group \"") +
name + "\":");

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}
return group_id;
}

inline herr_t h5g_get_num_objs(hid_t loc_id, hsize_t* num_objs) {
herr_t err = H5Gget_num_objs(loc_id, num_objs);
if (err < 0) {
HDF5ErrMapper::ToException<GroupException>(
std::string("Unable to count objects in existing group or file"));

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}

return err;
}


} // namespace detail
} // namespace HighFive
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