Skip to content

Commit

Permalink
Fixed issues with iterating/recursing through nodes in an HDF5 file, …
Browse files Browse the repository at this point in the history 
…when given relative paths
  • Loading branch information
@DavidAce
DavidAce committed Jul 21, 2022
1 parent c17ceae commit a1d8f08
Showing 1 changed file with 70 additions and 107 deletions.
177 changes: 70 additions & 107 deletions include/h5pp/details/h5ppHdf5.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -590,7 +590,7 @@ namespace h5pp::hdf5 {
"[h5pp::hid::h5f], [h5pp::hid::h5g], [h5pp::hid::h5o] or [hid_t]");
if constexpr(not h5pp::ndebug) {
if(not linkExists) linkExists = checkIfLinkExists(loc, linkPath, linkAccess);
if(not linkExists.value()) throw h5pp::runtime_error("Cannot open link [{}]: it does not exist [{}]", linkPath);
if(not linkExists.value()) throw h5pp::runtime_error("Cannot open link [{}]: it does not exist", linkPath);
}
if constexpr(std::is_same_v<h5x, hid::h5d>) h5pp::logger::log->trace("Opening dataset [{}]", linkPath);
if constexpr(std::is_same_v<h5x, hid::h5g>) h5pp::logger::log->trace("Opening group [{}]", linkPath);
Expand Down Expand Up @@ -1765,17 +1765,52 @@ namespace h5pp::hdf5 {
inline long maxDepth = -1;
inline bool symlinks = false;
inline std::string searchKey;
template<H5O_type_t ObjType>
[[nodiscard]] inline constexpr std::string_view getObjTypeName() {
if constexpr(ObjType == H5O_type_t::H5O_TYPE_DATASET) return "dataset";
if constexpr(ObjType == H5O_type_t::H5O_TYPE_GROUP) return "group";
if constexpr(ObjType == H5O_type_t::H5O_TYPE_UNKNOWN) return "unknown";
if constexpr(ObjType == H5O_type_t::H5O_TYPE_NAMED_DATATYPE) return "named datatype";
if constexpr(ObjType == H5O_type_t::H5O_TYPE_NTYPES) return "ntypes";
return "map"; // Only in HDF5 v 1.12
}
[[nodiscard]] inline std::string_view getObjTypeName(H5O_type_t type) {
if(type == H5O_type_t::H5O_TYPE_DATASET) return "dataset";
if(type == H5O_type_t::H5O_TYPE_GROUP) return "group";
if(type == H5O_type_t::H5O_TYPE_UNKNOWN) return "unknown";
if(type == H5O_type_t::H5O_TYPE_NAMED_DATATYPE) return "named datatype";
if(type == H5O_type_t::H5O_TYPE_NTYPES) return "ntypes";
return "map"; // Only in HDF5 v 1.12
}
template<H5L_type_t LinkType>
[[nodiscard]] inline constexpr std::string_view getLinkTypeName() {
if constexpr(LinkType == H5L_type_t::H5L_TYPE_ERROR) return "error";
if constexpr(LinkType == H5L_type_t::H5L_TYPE_HARD) return "hard";
if constexpr(LinkType == H5L_type_t::H5L_TYPE_SOFT) return "soft";
if constexpr(LinkType == H5L_type_t::H5L_TYPE_EXTERNAL) return "external";
if constexpr(LinkType == H5L_type_t::H5L_TYPE_MAX) return "max";
}
[[nodiscard]] inline std::string_view getObjTypeName(H5L_type_t type) {
if (type == H5L_type_t::H5L_TYPE_ERROR) return "error";
if (type == H5L_type_t::H5L_TYPE_HARD) return "hard";
if (type == H5L_type_t::H5L_TYPE_SOFT) return "soft";
if (type == H5L_type_t::H5L_TYPE_EXTERNAL) return "external";
if (type == H5L_type_t::H5L_TYPE_MAX) return "max";
}
template<H5O_type_t ObjType, typename InfoType>
inline herr_t matcher([[maybe_unused]] hid_t id, const char *name, [[maybe_unused]] const InfoType *info, void *opdata) {
// If object type is the one requested, and name matches the search key, then add it to the match list (a vector<string>)
// If the search depth is passed the depth specified, return immediately
// Return 0 to continue searching
// Return 1 to finish the search. Normally when we've reached max search hits.

// Skip symlinks if not asked for
if(not symlinks and (info->type == H5L_TYPE_SOFT or info->type == H5L_TYPE_EXTERNAL)) return 0;
std::string_view linkPath(name); // <-- This is the full path to the object that we are currently visiting.

// If this group is deeper than maxDepth, just return
if(maxDepth >= 0 and std::count(linkPath.begin(), linkPath.end(), '/') > maxDepth) return 0;
auto depth = std::count(linkPath.begin(), linkPath.end(), '/');
if(maxDepth >= 0 and depth > maxDepth) return 0;

// Get the name of the object without the full path, to match the searchKey
auto slashpos = linkPath.rfind('/');
Expand All @@ -1786,7 +1821,16 @@ namespace h5pp::hdf5 {
try {
if constexpr(std::is_same_v<InfoType, H5O_info_t>) {
if(info->type == ObjType or ObjType == H5O_TYPE_UNKNOWN) {
if(searchKey.empty() or linkName.find(searchKey) != std::string::npos) matchList->push_back(name);
if(searchKey.empty() or linkName.find(searchKey) != std::string::npos) {
if(depth >= 1 and not symlinks) { // H5Lget_info fails on the root "." or "/"
// Make sure not to include symbolic links if not asked for
H5L_info_t lInfo;
herr_t lerr = H5Lget_info(id, name, &lInfo, H5P_DEFAULT);
if(lerr < 0) throw h5pp::runtime_error("H5Lget_info failed on link [{}]", name);
if(lInfo.type == H5L_type_t::H5L_TYPE_SOFT or lInfo.type == H5L_TYPE_EXTERNAL) return 0;
}
matchList->push_back(name);
}
}
}

Expand All @@ -1802,7 +1846,10 @@ namespace h5pp::hdf5 {
#endif
/* clang-format on */
if(oInfo.type == ObjType or ObjType == H5O_TYPE_UNKNOWN) {
if(searchKey.empty() or linkName.find(searchKey) != std::string::npos) matchList->push_back(name);
if(searchKey.empty() or linkName.find(searchKey) != std::string::npos){
// Otherwise append the match
matchList->push_back(name);
}
}
} else {
if(searchKey.empty() or linkName.find(searchKey) != std::string::npos) { matchList->push_back(name); }
Expand All @@ -1812,94 +1859,12 @@ namespace h5pp::hdf5 {
return 1;
else
return 0;
} catch(...) { throw h5pp::logic_error(h5pp::format("Could not match object [{}] | loc_id [{}]", name, id)); }
}

template<H5O_type_t ObjType>
[[nodiscard]] inline constexpr std::string_view getObjTypeName() {
if constexpr(ObjType == H5O_type_t::H5O_TYPE_DATASET)
return "dataset";
else if constexpr(ObjType == H5O_type_t::H5O_TYPE_GROUP)
return "group";
else if constexpr(ObjType == H5O_type_t::H5O_TYPE_UNKNOWN)
return "unknown";
else if constexpr(ObjType == H5O_type_t::H5O_TYPE_NAMED_DATATYPE)
return "named datatype";
else if constexpr(ObjType == H5O_type_t::H5O_TYPE_NTYPES)
return "ntypes";
else
return "map"; // Only in HDF5 v 1.12
}

template<H5O_type_t ObjType, typename h5x>
herr_t H5L_custom_iterate_by_name(const h5x &loc,
std::string_view root,
std::vector<std::string> &matchList,
const hid::h5p &linkAccess = H5P_DEFAULT) {
H5Eset_auto(H5E_DEFAULT, nullptr, nullptr); // Silence the error we get from using index directly
H5O_info_t oInfo;
H5L_info_t lInfo;
/* clang-format off */
for(hsize_t idx = 0; idx < std::numeric_limits<hsize_t>::max(); idx++) {
std::string linkPath; // <-- This is the path to the object that we are currently visiting, relative to root
ssize_t namesize = H5Lget_name_by_idx(loc, root.data(), H5_index_t::H5_INDEX_NAME,
H5_iter_order_t::H5_ITER_NATIVE, idx,nullptr, linkPath.size(),linkAccess);
if(namesize <= 0) {
H5Eclear(H5E_DEFAULT);
break;
}
linkPath.resize(static_cast<size_t>(namesize));
namesize = H5Lget_name_by_idx(loc, root.data(), H5_index_t::H5_INDEX_NAME,
H5_iter_order_t::H5_ITER_NATIVE, idx,linkPath.data(),linkPath.size()+1,linkAccess);

// If this group is deeper than maxDepth, just return
if(maxDepth >= 0 and std::count(linkPath.begin(), linkPath.end(), '/') > maxDepth) return 0;

// Get the name of the object without the full path, to match the searchKey
auto slashpos = linkPath.rfind('/');
if(slashpos == std::string_view::npos) slashpos = 0;
auto linkName = linkPath.substr(slashpos);

if(ObjType == H5O_TYPE_UNKNOWN) {
// Accept based on name
if(searchKey.empty() or linkName.find(searchKey) != std::string::npos) matchList.emplace_back(linkPath);
if(maxHits > 0 and static_cast<long>(matchList.size()) >= maxHits) return 0;
} else {
// Check link type
herr_t lres = H5Lget_info_by_idx(loc, root.data(), H5_index_t::H5_INDEX_NAME, H5_iter_order_t::H5_ITER_NATIVE,idx, &lInfo, linkAccess);
if (lres < 0) {
H5Eclear(H5E_DEFAULT);
break;
}
switch(lInfo.type){
case H5L_type_t::H5L_TYPE_EXTERNAL:
case H5L_type_t::H5L_TYPE_SOFT: if(not symlinks) break;
default:;
}

// Name is not enough to establish a match. Check object type.
#if defined(H5Oget_info_by_idx_vers) && H5Oget_info_by_idx_vers >= 2
herr_t res = H5Oget_info_by_idx(loc, root.data(),
H5_index_t::H5_INDEX_NAME, H5_iter_order_t::H5_ITER_NATIVE,
idx, &oInfo, H5O_INFO_BASIC,linkAccess );
#else
herr_t res = H5Oget_info_by_idx(loc, root.data(),
H5_index_t::H5_INDEX_NAME, H5_iter_order_t::H5_ITER_NATIVE,
idx, &oInfo, linkAccess );
#endif
if(res < 0) {
H5Eclear(H5E_DEFAULT);
break;
}
if(oInfo.type == ObjType and (searchKey.empty() or linkName.find(searchKey) != std::string::npos))
matchList.emplace_back(linkPath);
if(maxHits > 0 and static_cast<long>(matchList.size()) >= maxHits) return 0;
}
} catch(const std::exception &ex) {
throw h5pp::logic_error("Could not match object [{}] | loc_id [{}] | reason: {}", name, id, ex.what());
}
/* clang-format on */
return 0;
}


template<H5O_type_t ObjType, typename h5x>
inline herr_t visit_by_name(const h5x &loc,
std::string_view root,
Expand All @@ -1910,28 +1875,26 @@ namespace h5pp::hdf5 {
"[h5pp::hid::h5f], [h5pp::hid::h5g], [h5pp::hid::h5o] or [hid_t]");
auto safe_root = util::safe_str(root);

if(internal::maxDepth == 0)
// Faster when we don't need to iterate recursively
return H5L_custom_iterate_by_name<ObjType>(loc, safe_root, matchList, linkAccess);

#if defined(H5Ovisit_by_name_vers) && H5Ovisit_by_name_vers >= 2
return H5Ovisit_by_name(loc,
safe_root.c_str(),
H5_INDEX_NAME,
H5_ITER_NATIVE,
internal::matcher<ObjType>,
&matchList,
H5O_INFO_BASIC,
linkAccess);
#else
return H5Ovisit_by_name(loc,
if constexpr (h5pp::type::sfinae::is_any_v<h5x, hid::h5f, hid::h5g>){
if(internal::maxDepth == 0){
// Faster when we don't need to iterate recursively
hsize_t idx = 0;
auto gid = openLink<hid::h5g>(loc, safe_root, std::nullopt, linkAccess);
return H5Literate(gid,
H5_index_t::H5_INDEX_NAME,
H5_iter_order_t::H5_ITER_NATIVE,
&idx,
internal::matcher<ObjType>,
&matchList);
}
}
return H5Lvisit_by_name(loc,
safe_root.c_str(),
H5_INDEX_NAME,
H5_ITER_NATIVE,
H5_index_t::H5_INDEX_NAME,
H5_iter_order_t::H5_ITER_NATIVE,
internal::matcher<ObjType>,
&matchList,
linkAccess);
#endif
}

}
Expand Down

0 comments on commit a1d8f08

Please sign in to comment.