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Change ccall wrapper signature of h5a_iterate and h5l_iterate #817

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Feb 12, 2021
Merged

Change ccall wrapper signature of h5a_iterate and h5l_iterate #817

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6 changes: 3 additions & 3 deletions gen/api_defs.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
@bind h5a_get_name_by_idx(loc_id::hid_t, obj_name::Cstring, index_type::Cint, order::Cint, idx::hsize_t, name::Ptr{UInt8}, size::Csize_t, lapl_id::hid_t)::Cssize_t "Error getting attribute name"
@bind h5a_get_space(attr_id::hid_t)::hid_t "Error getting attribute dataspace"
@bind h5a_get_type(attr_id::hid_t)::hid_t "Error getting attribute type"
@bind h5a_iterate2(obj_id::hid_t, idx_type::Cint, order::Cint, n::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})::herr_t error("Error iterating attributes in object ", h5i_get_name(obj_id))
@bind h5a_iterate2(obj_id::hid_t, idx_type::Cint, order::Cint, n::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Any)::herr_t error("Error iterating attributes in object ", h5i_get_name(obj_id))
@bind h5a_open(obj_id::hid_t, pathname::Ptr{UInt8}, aapl_id::hid_t)::hid_t error("Error opening attribute ", h5i_get_name(obj_id), "/", pathname)
@bind h5a_read(attr_id::hid_t, mem_type_id::hid_t, buf::Ptr{Cvoid})::herr_t error("Error reading attribute ", h5a_get_name(attr_id))
@bind h5a_write(attr_hid::hid_t, mem_type_id::hid_t, buf::Ptr{Cvoid})::herr_t "Error writing attribute data"
Expand Down Expand Up @@ -133,8 +133,8 @@
@bind h5l_get_name_by_idx(loc_id::hid_t, group_name::Ptr{UInt8}, index_field::Cint, order::Cint, n::hsize_t, name::Ptr{UInt8}, size::Csize_t, lapl_id::hid_t)::Cssize_t "Error getting object name"
# libhdf5 v1.10 provides the name H5Literate
# libhdf5 v1.12 provides the same under H5Literate1, and a newer interface on H5Literate2
@bind h5l_iterate(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})::herr_t error("Error iterating through links in group ", h5i_get_name(group_id)) (nothing, v"1.12")
@bind h5l_iterate1(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})::herr_t error("Error iterating through links in group ", h5i_get_name(group_id)) (v"1.12", nothing)
@bind h5l_iterate(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Any)::herr_t error("Error iterating through links in group ", h5i_get_name(group_id)) (nothing, v"1.12")
@bind h5l_iterate1(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Any)::herr_t error("Error iterating through links in group ", h5i_get_name(group_id)) (v"1.12", nothing)

###
### Object Interface
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12 changes: 6 additions & 6 deletions src/api.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -242,12 +242,12 @@ function h5a_get_type(attr_id)
end

"""
h5a_iterate(obj_id::hid_t, idx_type::Cint, order::Cint, n::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})
h5a_iterate(obj_id::hid_t, idx_type::Cint, order::Cint, n::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Any)

See `libhdf5` documentation for [`H5Aiterate2`](https://portal.hdfgroup.org/display/HDF5/H5A_ITERATE2).
"""
function h5a_iterate(obj_id, idx_type, order, n, op, op_data)
var"#status#" = ccall((:H5Aiterate2, libhdf5), herr_t, (hid_t, Cint, Cint, Ptr{hsize_t}, Ptr{Cvoid}, Ptr{Cvoid}), obj_id, idx_type, order, n, op, op_data)
var"#status#" = ccall((:H5Aiterate2, libhdf5), herr_t, (hid_t, Cint, Cint, Ptr{hsize_t}, Ptr{Cvoid}, Any), obj_id, idx_type, order, n, op, op_data)
var"#status#" < 0 && error("Error iterating attributes in object ", h5i_get_name(obj_id))
return nothing
end
Expand Down Expand Up @@ -859,25 +859,25 @@ end

@static if _libhdf5_build_ver < v"1.12"
@doc """
h5l_iterate(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})
h5l_iterate(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Any)

See `libhdf5` documentation for [`H5Literate`](https://portal.hdfgroup.org/display/HDF5/H5L_ITERATE).
"""
function h5l_iterate(group_id, idx_type, order, idx, op, op_data)
var"#status#" = ccall((:H5Literate, libhdf5), herr_t, (hid_t, Cint, Cint, Ptr{hsize_t}, Ptr{Cvoid}, Ptr{Cvoid}), group_id, idx_type, order, idx, op, op_data)
var"#status#" = ccall((:H5Literate, libhdf5), herr_t, (hid_t, Cint, Cint, Ptr{hsize_t}, Ptr{Cvoid}, Any), group_id, idx_type, order, idx, op, op_data)
var"#status#" < 0 && error("Error iterating through links in group ", h5i_get_name(group_id))
return nothing
end
end

@static if v"1.12" ≤ _libhdf5_build_ver
@doc """
h5l_iterate(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})
h5l_iterate(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Any)

See `libhdf5` documentation for [`H5Literate1`](https://portal.hdfgroup.org/display/HDF5/H5L_ITERATE1).
"""
function h5l_iterate(group_id, idx_type, order, idx, op, op_data)
var"#status#" = ccall((:H5Literate1, libhdf5), herr_t, (hid_t, Cint, Cint, Ptr{hsize_t}, Ptr{Cvoid}, Ptr{Cvoid}), group_id, idx_type, order, idx, op, op_data)
var"#status#" = ccall((:H5Literate1, libhdf5), herr_t, (hid_t, Cint, Cint, Ptr{hsize_t}, Ptr{Cvoid}, Any), group_id, idx_type, order, idx, op, op_data)
var"#status#" < 0 && error("Error iterating through links in group ", h5i_get_name(group_id))
return nothing
end
Expand Down
20 changes: 2 additions & 18 deletions src/api_helpers.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -68,15 +68,7 @@ julia> HDF5.h5a_iterate(obj, HDF5.H5_INDEX_NAME, HDF5.H5_ITER_INC) do loc, name,
function h5a_iterate(@nospecialize(f), obj_id, idx_type, order, idx = 0)
idxref = Ref{hsize_t}(idx)
fptr = @cfunction(h5a_iterate_helper, herr_t, (hid_t, Ptr{Cchar}, Ptr{H5A_info_t}, Any))
userf = Ref{Any}(f)
if VERSION < v"1.6.0-DEV.1038"
# unsafe_convert(Ptr{Cvoid}, ::RefValue{Any}) returns pointer to RefValue instead
# of data --- see JuliaLang/julia#37591
userfptr = unsafe_load(Ptr{Ptr{Cvoid}}(unsafe_convert(Ptr{Any}, userf)))
GC.@preserve userf h5a_iterate(obj_id, idx_type, order, idxref, fptr, userfptr)
else
GC.@preserve userf h5a_iterate(obj_id, idx_type, order, idxref, fptr, userf)
end
h5a_iterate(obj_id, idx_type, order, idxref, fptr, f)
return idxref[]
end

Expand Down Expand Up @@ -204,15 +196,7 @@ julia> HDF5.h5l_iterate(hfile, HDF5.H5_INDEX_NAME, HDF5.H5_ITER_INC) do group, n
function h5l_iterate(@nospecialize(f), group_id, idx_type, order, idx = 0)
idxref = Ref{hsize_t}(idx)
fptr = @cfunction(h5l_iterate_helper, herr_t, (hid_t, Ptr{Cchar}, Ptr{H5L_info_t}, Any))
userf = Ref{Any}(f)
if VERSION < v"1.6.0-DEV.1038"
# unsafe_convert(Ptr{Cvoid}, ::RefValue{Any}) returns pointer to RefValue instead
# of data --- see JuliaLang/julia#37591
userfptr = unsafe_load(Ptr{Ptr{Cvoid}}(unsafe_convert(Ptr{Any}, userf)))
GC.@preserve userf h5l_iterate(group_id, idx_type, order, idxref, fptr, userfptr)
else
GC.@preserve userf h5l_iterate(group_id, idx_type, order, idxref, fptr, userf)
end
h5l_iterate(group_id, idx_type, order, idxref, fptr, f)
return idxref[]
end

Expand Down