<commit_before># cython: profile=False

# This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 <NAME> and contributors
#
# License:  Standard 3-clause BSD; see "license.txt" for full license terms
#           and contributor agreement.

"""
    Proxy functions for read/write, to work around the HDF5 bogus type issue.
"""

cdef enum copy_dir:
    H5PY_SCATTER = 0,
    H5PY_GATHER

cdef herr_t attr_rw(hid_t attr, hid_t mtype, void *progbuf, int read) except -1:

    cdef htri_t need_bkg
    cdef hid_t atype = -1
    cdef hid_t aspace = -1
    cdef hsize_t npoints

    cdef size_t msize, asize
    cdef void* conv_buf = NULL
    cdef void* back_buf = NULL

    try:
        atype = H5Aget_type(attr)

        if not (needs_proxy(atype) or needs_proxy(mtype)):
            if read:
                H5Aread(attr, mtype, progbuf)
            else:
                H5Awrite(attr, mtype, progbuf)

        else:
            
            asize = H5Tget_size(atype)
            msize = H5Tget_size(mtype)
            aspace = H5Aget_space(attr)
            npoints = H5Sget_select_npoints(aspace)

            conv_buf = create_buffer(asize, msize, npoints)
            
            if read:
                need_bkg = needs_bkg_buffer(atype, mtype)
            else:
                need_bkg = needs_bkg_buffer(mtype, atype)
            if need_bkg:
                back_buf = malloc(msize*npoints)
                memcpy(back_buf, progbuf, msize*npoints)

            if read:
                H5Aread(attr, atype, conv_buf)
                H5Tconvert(atype, mtype, npoints, conv_buf, back_buf, H5P_DEFAULT)
                memcpy(progbuf, conv_buf, msize*npoints)
            else:
                memcpy(conv_buf, progbuf, msize*npoints)
                H5Tconvert(mtype, atype, npoints, conv_buf, back_buf, H5P_DEFAULT)
                H5Awrite(attr, atype, conv_buf)
                H5Dvlen_reclaim(atype, aspace, H5P_DEFAULT, conv_buf)

    finally:
        free(conv_buf)
        free(back_buf)
        if atype > 0:
            H5Tclose(atype)
        if aspace > 0:
            H5Sclose(aspace)

    return 0

# =============================================================================
# Proxy functions to safely release the GIL around read/write operations

cdef herr_t H5PY_H5Dread(hid_t dset, hid_t mtype, hid_t mspace,
                        hid_t fspace, hid_t dxpl, void* buf) except -1:
    cdef herr_t retval
    #with nogil:
    retval = H5Dread(dset, mtype, mspace, fspace, dxpl, buf)
    if retval < 0:
        return -1
    return retval

cdef herr_t H5PY_H5Dwrite(hid_t dset, hid_t mtype, hid_t mspace,
                        hid_t fspace, hid_t dxpl, void* buf) except -1:
    cdef herr_t retval
    #with nogil:
    retval = H5Dwrite(dset, mtype, mspace, fspace, dxpl, buf)
    if retval < 0:
        return -1
    return retval

# =============================================================================
# Proxy for vlen buf workaround

cdef herr_t dset_rw(hid_t dset, hid_t mtype, hid_t mspace, hid_t fspace,
                    hid_t dxpl, void* progbuf, int read) except -1:

    cdef htri_t need_bkg
    cdef hid_t dstype = -1      # Dataset datatype
    cdef hid_t dspace = -1      # Dataset dataspace
    cdef hid_t cspace = -1      # Temporary contiguous dataspaces

    cdef void* back_buf = NULL
    cdef void* conv_buf = NULL
    cdef hsize_t npoints

    try:
        dstype = H5Dget_type(dset)

        if not (needs_proxy(dstype) or needs_proxy(mtype)):
            if read:
                H5PY_H5Dread(dset, mtype, mspace, fspace, dxpl, progbuf)
            else:
                H5PY_H5Dwrite(dset, mtype, mspace, fspace, dxpl, progbuf)
        else:

            if mspace == H5S_ALL and fspace != H5S_ALL:
                mspace = fspace
            elif mspace != H5S_ALL and fspace == H5S_ALL:
                fspace = mspace
            elif mspace == H5S_ALL and fspace == H5S_ALL:
                fspace = mspace = dspace = H5Dget_space(dset)

            npoints = H5Sget_select_npoints(mspace)
            cspace = H5Screate_simple(1, &npoints, NULL)

            conv_buf = create_buffer(H5Tget_size(dstype), H5Tget_size(mtype), npoints)

            # Only create a (contiguous) backing buffer if absolutely
            # necessary. Note this buffer always has memory type.
            if read:
                need_bkg = needs_bkg_buffer(dstype, mtype)
            else:
                need_bkg = needs_bkg_buffer(mtype, dstype)
            if need_bkg:
                back_buf = create_buffer(H5Tget_size(dstype), H5Tget_size(mtype), npoints)
                h5py_copy(mtype, mspace, back_buf, progbuf, H5PY_GATHER)

            if read:
                H5PY_H5Dread(dset, dstype, cspace, fspace, dxpl, conv_buf)
                H5Tconvert(dstype, mtype, npoints, conv_buf, back_buf, dxpl)
                h5py_copy(mtype, mspace, conv_buf, progbuf, H5PY_SCATTER)
            else:
                h5py_copy(mtype, mspace, conv_buf, progbuf, H5PY_GATHER)
                H5Tconvert(mtype, dstype, npoints, conv_buf, back_buf, dxpl)
                H5PY_H5Dwrite(dset, dstype, cspace, fspace, dxpl, conv_buf)
                H5Dvlen_reclaim(dstype, cspace, H5P_DEFAULT, conv_buf)
 
    finally:
        free(back_buf)
        free(conv_buf)
        if dstype > 0:
            H5Tclose(dstype)
        if dspace > 0:
            H5Sclose(dspace)
        if cspace > 0:
            H5Sclose(cspace)

    return 0

cdef void* create_buffer(size_t ipt_size, size_t opt_size, size_t nl) except NULL:
    
    cdef size_t final_size
    cdef void* buf

    if ipt_size >= opt_size:
        final_size = ipt_size*nl
    else:
        final_size = opt_size*nl
        
    buf = malloc(final_size)
    if buf == NULL:
        raise MemoryError("Failed to allocate conversion buffer")

    return buf

# =============================================================================
# Scatter/gather routines

ctypedef struct h5py_scatter_t:
    size_t i
    size_t elsize
    void* buf

cdef herr_t h5py_scatter_cb(void* elem, hid_t type_id, unsigned ndim,
                hsize_t *point, void *operator_data) except -1:

    cdef h5py_scatter_t* info = <h5py_scatter_t*>operator_data
   
    memcpy(elem, (<char*>info[0].buf)+((info[0].i)*(info[0].elsize)), 
           info[0].elsize)
    
    info[0].i += 1

    return 0

cdef herr_t h5py_gather_cb(void* elem, hid_t type_id, unsigned ndim,
                hsize_t *point, void *operator_data) except -1:

    cdef h5py_scatter_t* info = <h5py_scatter_t*>operator_data
   
    memcpy((<char*>info[0].buf)+((info[0].i)*(info[0].elsize)), elem, 
            info[0].elsize)
    
    info[0].i += 1

    return 0

# Copy between a contiguous and non-contiguous buffer, with the layout
# of the latter specified by a dataspace selection.
cdef herr_t h5py_copy(hid_t tid, hid_t space, void* contig, void* noncontig,
                 copy_dir op) except -1:

    cdef h5py_scatter_t info
    cdef hsize_t elsize

    elsize = H5Tget_size(tid)

    info.i = 0
    info.elsize = elsize
    info.buf = contig

    if op == H5PY_SCATTER:
        H5Diterate(noncontig, tid, space, h5py_scatter_cb, &info)
    elif op == H5PY_GATHER:
        H5Diterate(noncontig, tid, space, h5py_gather_cb, &info)
    else:
        raise RuntimeError("Illegal direction")

    return 0

# =============================================================================
# VLEN support routines

cdef htri_t needs_bkg_buffer(hid_t src, hid_t dst) except -1:
    
    cdef H5T_cdata_t *info = NULL

    if H5Tdetect_class(src, H5T_COMPOUND) or H5Tdetect_class(dst, H5T_COMPOUND):
        return 1

    try:
        H5Tfind(src, dst, &info)
    except:
        print "Failed to find converter for %s -> %s" % (H5Tget_size(src), H5Tget_tag(dst))
        raise

    if info[0].need_bkg == H5T_BKG_YES:
        return 1

    return 0

# Determine if the given type requires proxy buffering
cdef htri_t needs_proxy(hid_t tid) except -1:
    
    cdef H5T_class_t cls
    cdef hid_t supertype
    cdef int i, n
    cdef htri_t result

    cls = H5Tget_class(tid)

    if cls == H5T_VLEN or cls == H5T_REFERENCE:
        return 1

    elif cls == H5T_STRING:
        return H5Tis_variable_str(tid)

    elif cls == H5T_ARRAY:
        
        supertype = H5Tget_super(tid)
        try:
            return needs_proxy(supertype)
        finally:
            H5Tclose(supertype)

    elif cls == H5T_COMPOUND:

        n = H5Tget_nmembers(tid)
        for i from 0<=i<n:
            supertype = H5Tget_member_type(tid, i)
            try:
                result = needs_proxy(supertype)
                if result > 0:
                    return 1
            finally:
                H5Tclose(supertype)
        return 0

    return 0
<commit_msg>Update proxy writer for issue 372<commit_after># cython: profile=False

# This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 <NAME> and contributors
#
# License:  Standard 3-clause BSD; see "license.txt" for full license terms
#           and contributor agreement.

"""
    Proxy functions for read/write, to work around the HDF5 bogus type issue.
"""

cdef enum copy_dir:
    H5PY_SCATTER = 0,
    H5PY_GATHER

cdef herr_t attr_rw(hid_t attr, hid_t mtype, void *progbuf, int read) except -1:

    cdef htri_t need_bkg
    cdef hid_t atype = -1
    cdef hid_t aspace = -1
    cdef hsize_t npoints

    cdef size_t msize, asize
    cdef void* conv_buf = NULL
    cdef void* back_buf = NULL

    try:
        atype = H5Aget_type(attr)

        if not (needs_proxy(atype) or needs_proxy(mtype)):
            if read:
                H5Aread(attr, mtype, progbuf)
            else:
                H5Awrite(attr, mtype, progbuf)

        else:
            
            asize = H5Tget_size(atype)
            msize = H5Tget_size(mtype)
            aspace = H5Aget_space(attr)
            npoints = H5Sget_select_npoints(aspace)

            conv_buf = create_buffer(asize, msize, npoints)
            
            if read:
                need_bkg = needs_bkg_buffer(atype, mtype)
            else:
                need_bkg = needs_bkg_buffer(mtype, atype)
            if need_bkg:
                back_buf = malloc(msize*npoints)
                memcpy(back_buf, progbuf, msize*npoints)

            if read:
                H5Aread(attr, atype, conv_buf)
                H5Tconvert(atype, mtype, npoints, conv_buf, back_buf, H5P_DEFAULT)
                memcpy(progbuf, conv_buf, msize*npoints)
            else:
                memcpy(conv_buf, progbuf, msize*npoints)
                H5Tconvert(mtype, atype, npoints, conv_buf, back_buf, H5P_DEFAULT)
                H5Awrite(attr, atype, conv_buf)
                H5Dvlen_reclaim(atype, aspace, H5P_DEFAULT, conv_buf)

    finally:
        free(conv_buf)
        free(back_buf)
        if atype > 0:
            H5Tclose(atype)
        if aspace > 0:
            H5Sclose(aspace)

    return 0

# =============================================================================
# Proxy functions to safely release the GIL around read/write operations

cdef herr_t H5PY_H5Dread(hid_t dset, hid_t mtype, hid_t mspace,
                        hid_t fspace, hid_t dxpl, void* buf) except -1:
    cdef herr_t retval
    #with nogil:
    retval = H5Dread(dset, mtype, mspace, fspace, dxpl, buf)
    if retval < 0:
        return -1
    return retval

cdef herr_t H5PY_H5Dwrite(hid_t dset, hid_t mtype, hid_t mspace,
                        hid_t fspace, hid_t dxpl, void* buf) except -1:
    cdef herr_t retval
    #with nogil:
    retval = H5Dwrite(dset, mtype, mspace, fspace, dxpl, buf)
    if retval < 0:
        return -1
    return retval

# =============================================================================
# Proxy for vlen buf workaround


cdef herr_t dset_rw(hid_t dset, hid_t mtype, hid_t mspace, hid_t fspace,
                    hid_t dxpl, void* progbuf, int read) except -1:

    cdef htri_t need_bkg
    cdef hid_t dstype = -1      # Dataset datatype
    cdef hid_t rawdstype = -1
    cdef hid_t dspace = -1      # Dataset dataspace
    cdef hid_t cspace = -1      # Temporary contiguous dataspaces

    cdef void* back_buf = NULL
    cdef void* conv_buf = NULL
    cdef hsize_t npoints

    try:
        # Issue 372: when a compound type is involved, using the dataset type
        # may result in uninitialized data being sent to H5Tconvert for fields
        # not present in the memory type.  Limit the type used for the dataset
        # to only those fields present in the memory type.  We can't use the
        # memory type directly because of course that triggers HDFFV-1063.
        if (H5Tget_class(mtype) == H5T_COMPOUND) and (not read):
            rawdstype = H5Dget_type(dset)
            dstype = make_reduced_type(mtype, rawdstype)
            H5Tclose(rawdstype)
        else:
            dstype = H5Dget_type(dset)

        if not (needs_proxy(dstype) or needs_proxy(mtype)):
            if read:
                H5PY_H5Dread(dset, mtype, mspace, fspace, dxpl, progbuf)
            else:
                H5PY_H5Dwrite(dset, mtype, mspace, fspace, dxpl, progbuf)
        else:

            if mspace == H5S_ALL and fspace != H5S_ALL:
                mspace = fspace
            elif mspace != H5S_ALL and fspace == H5S_ALL:
                fspace = mspace
            elif mspace == H5S_ALL and fspace == H5S_ALL:
                fspace = mspace = dspace = H5Dget_space(dset)

            npoints = H5Sget_select_npoints(mspace)
            cspace = H5Screate_simple(1, &npoints, NULL)

            conv_buf = create_buffer(H5Tget_size(dstype), H5Tget_size(mtype), npoints)

            # Only create a (contiguous) backing buffer if absolutely
            # necessary. Note this buffer always has memory type.
            if read:
                need_bkg = needs_bkg_buffer(dstype, mtype)
            else:
                need_bkg = needs_bkg_buffer(mtype, dstype)
            if need_bkg:
                back_buf = create_buffer(H5Tget_size(dstype), H5Tget_size(mtype), npoints)
                h5py_copy(mtype, mspace, back_buf, progbuf, H5PY_GATHER)

            if read:
                H5PY_H5Dread(dset, dstype, cspace, fspace, dxpl, conv_buf)
                H5Tconvert(dstype, mtype, npoints, conv_buf, back_buf, dxpl)
                h5py_copy(mtype, mspace, conv_buf, progbuf, H5PY_SCATTER)
            else:
                h5py_copy(mtype, mspace, conv_buf, progbuf, H5PY_GATHER)
                H5Tconvert(mtype, dstype, npoints, conv_buf, back_buf, dxpl)
                H5PY_H5Dwrite(dset, dstype, cspace, fspace, dxpl, conv_buf)
                H5Dvlen_reclaim(dstype, cspace, H5P_DEFAULT, conv_buf)
 
    finally:
        free(back_buf)
        free(conv_buf)
        if dstype > 0:
            H5Tclose(dstype)
        if dspace > 0:
            H5Sclose(dspace)
        if cspace > 0:
            H5Sclose(cspace)

    return 0


cdef hid_t make_reduced_type(hid_t mtype, hid_t dstype):
    # Go through dstype, pick out the fields which also appear in mtype, and
    # return a new compound type with the fields packed together
    # See also: issue 372

    cdef hid_t newtype, temptype
    cdef hsize_t newtype_size, offset

    # Make a list of all names in the memory type.
    mtype_fields = []
    for idx in xrange(H5Tget_nmembers(mtype)):
        mtype_fields.append(H5Tget_member_name(mtype, idx))

    # First pass: add up the sizes of matching fields so we know how large a
    # type to make
    newtype_size = 0
    for idx in xrange(H5Tget_nmembers(dstype)):
        name = H5Tget_member_name(dstype, idx)
        if name not in mtype_fields:
            continue
        temptype = H5Tget_member_type(dstype, idx)
        newtype_size += H5Tget_size(temptype)
        H5Tclose(temptype)

    newtype = H5Tcreate(H5T_COMPOUND, newtype_size)

    # Second pass: pick out the matching fields and pack them in the new type
    offset = 0
    for idx in xrange(H5Tget_nmembers(dstype)):
        name = H5Tget_member_name(dstype, idx)
        if name not in mtype_fields:
            continue
        temptype = H5Tget_member_type(dstype, idx)
        H5Tinsert(newtype, name, offset, temptype)
        offset += H5Tget_size(temptype)
        H5Tclose(temptype)

    return newtype


cdef void* create_buffer(size_t ipt_size, size_t opt_size, size_t nl) except NULL:
    
    cdef size_t final_size
    cdef void* buf

    if ipt_size >= opt_size:
        final_size = ipt_size*nl
    else:
        final_size = opt_size*nl
        
    buf = malloc(final_size)
    if buf == NULL:
        raise MemoryError("Failed to allocate conversion buffer")

    return buf

# =============================================================================
# Scatter/gather routines

ctypedef struct h5py_scatter_t:
    size_t i
    size_t elsize
    void* buf

cdef herr_t h5py_scatter_cb(void* elem, hid_t type_id, unsigned ndim,
                hsize_t *point, void *operator_data) except -1:

    cdef h5py_scatter_t* info = <h5py_scatter_t*>operator_data
   
    memcpy(elem, (<char*>info[0].buf)+((info[0].i)*(info[0].elsize)), 
           info[0].elsize)
    
    info[0].i += 1

    return 0

cdef herr_t h5py_gather_cb(void* elem, hid_t type_id, unsigned ndim,
                hsize_t *point, void *operator_data) except -1:

    cdef h5py_scatter_t* info = <h5py_scatter_t*>operator_data
   
    memcpy((<char*>info[0].buf)+((info[0].i)*(info[0].elsize)), elem, 
            info[0].elsize)
    
    info[0].i += 1

    return 0

# Copy between a contiguous and non-contiguous buffer, with the layout
# of the latter specified by a dataspace selection.
cdef herr_t h5py_copy(hid_t tid, hid_t space, void* contig, void* noncontig,
                 copy_dir op) except -1:

    cdef h5py_scatter_t info
    cdef hsize_t elsize

    elsize = H5Tget_size(tid)

    info.i = 0
    info.elsize = elsize
    info.buf = contig

    if op == H5PY_SCATTER:
        H5Diterate(noncontig, tid, space, h5py_scatter_cb, &info)
    elif op == H5PY_GATHER:
        H5Diterate(noncontig, tid, space, h5py_gather_cb, &info)
    else:
        raise RuntimeError("Illegal direction")

    return 0

# =============================================================================
# VLEN support routines

cdef htri_t needs_bkg_buffer(hid_t src, hid_t dst) except -1:
    
    cdef H5T_cdata_t *info = NULL

    if H5Tdetect_class(src, H5T_COMPOUND) or H5Tdetect_class(dst, H5T_COMPOUND):
        return 1

    try:
        H5Tfind(src, dst, &info)
    except:
        print "Failed to find converter for %s -> %s" % (H5Tget_size(src), H5Tget_tag(dst))
        raise

    if info[0].need_bkg == H5T_BKG_YES:
        return 1

    return 0

# Determine if the given type requires proxy buffering
cdef htri_t needs_proxy(hid_t tid) except -1:
    
    cdef H5T_class_t cls
    cdef hid_t supertype
    cdef int i, n
    cdef htri_t result

    cls = H5Tget_class(tid)

    if cls == H5T_VLEN or cls == H5T_REFERENCE:
        return 1

    elif cls == H5T_STRING:
        return H5Tis_variable_str(tid)

    elif cls == H5T_ARRAY:
        
        supertype = H5Tget_super(tid)
        try:
            return needs_proxy(supertype)
        finally:
            H5Tclose(supertype)

    elif cls == H5T_COMPOUND:

        n = H5Tget_nmembers(tid)
        for i from 0<=i<n:
            supertype = H5Tget_member_type(tid, i)
            try:
                result = needs_proxy(supertype)
                if result > 0:
                    return 1
            finally:
                H5Tclose(supertype)
        return 0

    return 0

{'fraction_non_alphanumeric': 0.10646368602063525, 'fraction_numerical': 0.018409872547036212, 'mean_word_length': 2.2193096711169003, 'pattern_counts': {'":': 0, '<': 21, '<?xml version=': 0, '>': 29, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1404821', 'n_tokens_mistral': 7051, 'n_tokens_neox': 6733, 'n_words': 1743}