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#############################################################################
##
## Copyright 2016 Novartis Institutes for BioMedical Research Inc.
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
##
## http://www.apache.org/licenses/LICENSE-2.0
##
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
##
#############################################################################
## we replace nested struct definition by unnested ones
## the nested definitions are written into HelperStructs.h
fileReplace <- function(filename, what, replace, fixed=FALSE) {
if(!file.exists(filename)) {
stop(paste("File", filename, "does not exist"))
}
L <- readLines(filename)
L <- paste(L, collapse="\n")
## collapse multiple spaces to single space
replace <- paste(replace, collapse="\n")
## check if it can be found
if(!grepl(what, L, fixed=fixed)) {
stop(paste("In File:", filename, "\nCould not find:\n", what, "\n\nTo be replaced with:\n", replace))
}
L <- gsub(what, replace, L, fixed=fixed)
cat(c(L, ""), file=filename, collapse="\n")
}
################################
### Replace H5F_info2_t
################################
H5Fpublic_what <- "typedef struct H5F_info2_t \\{.*\\} H5F_info2_t;"
H5Fpublic_replace <- "typedef struct H5F_info2_t {
H5F_info2_super_t super;
H5F_info2_free_t free;
H5F_info2_sohm_t sohm;
} H5F_info2_t;"
H5Fpublic_file <- "src_nocomments/H5Fpublic.h.nocomments"
fileReplace(H5Fpublic_file, H5Fpublic_what, H5Fpublic_replace)
################################
### Replace H5F_info1_t
################################
H5Fpublic_what <- "typedef struct H5F_info1_t \\{.*\\} H5F_info1_t;"
H5Fpublic_replace <- "typedef struct H5F_info1_t {
hsize_t super_ext_size;
H5F_info1_helper_t sohm;
} H5F_info1_t;"
H5Fpublic_file <- "src_nocomments/H5Fpublic.h.nocomments"
fileReplace(H5Fpublic_file, H5Fpublic_what, H5Fpublic_replace)
################################
### Replace H5O_hdfr_info_t
################################
## do the same for the other 2 structs in H5Opublic.h.nocomments
H5Opublic_file <- "src_nocomments/H5Opublic.h.nocomments"
H5Opublic_hdr_info_what <- "typedef struct H5O_hdr_info_t \\{.*\\} H5O_hdr_info_t;"
H5Opublic_hdr_info_replace <- "typedef struct H5O_hdr_info_t {
unsigned version;
unsigned nmesgs;
unsigned nchunks;
unsigned flags;
H5O_hdr_info_helper_space_t space;
H5O_hdr_info_helper_msg_t mesg;
} H5O_hdr_info_t;"
fileReplace(H5Opublic_file, H5Opublic_hdr_info_what, H5Opublic_hdr_info_replace)
################################
### Replace H5O_info_t
################################
H5Opublic_file <- "src_nocomments/H5Opublic.h.nocomments"
H5Opublic_info_what <- "typedef struct H5O_info_t \\{.*\\} H5O_info_t;"
H5Opublic_info_replace <- "typedef struct H5O_info_t {
unsigned long fileno;
haddr_t addr;
H5O_type_t type;
unsigned rc;
time_t atime;
time_t mtime;
time_t ctime;
time_t btime;
hsize_t num_attrs;
H5O_hdr_info_t hdr;
H5O_info_helper_t meta_size;
} H5O_info_t;"
fileReplace(H5Opublic_file, H5Opublic_info_what, H5Opublic_info_replace)
################################
### Replace H5L_info_t
################################
H5Lpublic_file <- "src_nocomments/H5Lpublic.h.nocomments"
H5Lpublic_what <- "typedef struct \\{.*\\} H5L_info_t;"
H5Lpublic_replace <- "typedef struct H5L_info_t {
H5L_type_t type;
hbool_t corder_valid;
int64_t corder;
H5T_cset_t cset;
H5L_info_helper_t u;
} H5L_info_t;"
fileReplace(H5Lpublic_file, H5Lpublic_what, H5Lpublic_replace)
################################
### Replace H5C_cache_incr_mode
################################
H5Cpublic_file <- "src_nocomments/H5Cpublic.h.nocomments"
H5Cpublic_what <- "enum H5C_cache_incr_mode
{
H5C_incr__off,
H5C_incr__threshold
};
enum H5C_cache_flash_incr_mode
{
H5C_flash_incr__off,
H5C_flash_incr__add_space
};
enum H5C_cache_decr_mode
{
H5C_decr__off,
H5C_decr__threshold,
H5C_decr__age_out,
H5C_decr__age_out_with_threshold
};"
H5Cpublic_replace <- "typedef enum H5C_cache_incr_mode
{
H5C_incr__off,
H5C_incr__threshold
} H5C_cache_incr_mode;
typedef enum H5C_cache_flash_incr_mode
{
H5C_flash_incr__off,
H5C_flash_incr__add_space
} H5C_cache_flash_incr_mode;
typedef enum H5C_cache_decr_mode
{
H5C_decr__off,
H5C_decr__threshold,
H5C_decr__age_out,
H5C_decr__age_out_with_threshold
} H5C_cache_decr_mode;"
fileReplace(H5Cpublic_file, H5Cpublic_what, H5Cpublic_replace, fixed=TRUE)
################################
### Replace H5FD_free_t
################################
## delete something in H5FD
H5FDpublic_file <- "src_nocomments/H5FDpublic.h.nocomments"
H5FDpublic_what <- "typedef struct H5FD_free_t \\{.*\\} H5FD_free_t;"
H5FDpublic_replace <- ""
fileReplace(H5FDpublic_file, H5FDpublic_what, H5FDpublic_replace)
################################
### Replace H5FD_file_image_callbacks_t
################################
H5FDpublic_what <- "typedef struct \\{.*\\} H5FD_file_image_callbacks_t;"
fileReplace(H5FDpublic_file, H5FDpublic_what, "")
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