diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/lib/tng_io.c | 274 | ||||
| -rw-r--r-- | src/lib/tng_io.h | 35 | ||||
| -rw-r--r-- | src/tests/tng_io_testing.c | 16 |
3 files changed, 190 insertions, 135 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 1f01f81..00bf730 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -370,7 +370,8 @@ static tng_function_status tng_read_block_header static tng_function_status tng_write_block_header (tng_trajectory_t tng_data, - struct tng_gen_block *block, write_mode mode) + struct tng_gen_block *block, const tng_write_mode mode, + const tng_hash_mode hash_mode) { int name_len, offset = 0; @@ -414,7 +415,10 @@ static tng_function_status tng_write_block_header name_len = min(strlen(block->name) + 1, TNG_MAX_STR_LEN); - tng_generate_block_hash(block); + if(hash_mode == TNG_USE_HASH) + { + tng_generate_block_hash(block); + } /* Calculate the size of the header to write */ block->header_contents_size = sizeof(block->header_contents_size) + @@ -511,7 +515,8 @@ static tng_function_status tng_write_block_header static tng_function_status tng_read_general_info_block - (tng_trajectory_t tng_data, struct tng_gen_block *block) + (tng_trajectory_t tng_data, struct tng_gen_block *block, + const tng_hash_mode hash_mode) { int len, offset = 0; tng_bool same_hash; @@ -543,18 +548,20 @@ static tng_function_status tng_read_general_info_block /* FIXME: Does not check if the size of the contents matches the expected * size or if the contents can be read. */ - - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + if(hash_mode == TNG_USE_HASH) { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } - if(same_hash != TRUE) - { - printf("General info block contents corrupt. Hashes do not match. " - "%s: %d\n", - __FILE__, __LINE__); -// return(TNG_FAILURE); + if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + { + printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); + return(TNG_FAILURE); + } + if(same_hash != TRUE) + { + printf("General info block contents corrupt. Hashes do not match. " + "%s: %d\n", + __FILE__, __LINE__); + // return(TNG_FAILURE); + } } len = min(strlen(block->block_contents) + 1, TNG_MAX_STR_LEN); @@ -696,7 +703,8 @@ static tng_function_status tng_read_general_info_block static tng_function_status tng_write_general_info_block (tng_trajectory_t tng_data, struct tng_gen_block *block, - write_mode mode) + const tng_write_mode mode, + const tng_hash_mode hash_mode) { int program_name_len, forcefield_name_len, user_name_len; int computer_name_len, pgp_signature_len; @@ -783,7 +791,7 @@ static tng_function_status tng_write_general_info_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -927,7 +935,7 @@ static tng_function_status tng_write_general_info_block } - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -949,7 +957,8 @@ static tng_function_status tng_write_general_info_block /* FIXME: Update this according to the new specs */ static tng_function_status tng_read_molecules_block (tng_trajectory_t tng_data, - struct tng_gen_block *block) + struct tng_gen_block *block, + const tng_hash_mode hash_mode) { int i, j, k, l, len, offset = 0; struct tng_molecule *molecule; @@ -990,17 +999,20 @@ static tng_function_status tng_read_molecules_block /* FIXME: Does not check if the size of the contents matches the expected * size or if the contents can be read. */ - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) - { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } - if(same_hash != TRUE) + if(hash_mode == TNG_USE_HASH) { - printf("Molecules block contents corrupt. Hashes do not match. " - "%s: %d\n", - __FILE__, __LINE__); -// return(TNG_FAILURE); + if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + { + printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); + return(TNG_FAILURE); + } + if(same_hash != TRUE) + { + printf("Molecules block contents corrupt. Hashes do not match. " + "%s: %d\n", + __FILE__, __LINE__); + // return(TNG_FAILURE); + } } memcpy(&tng_data->n_molecules, block->block_contents, @@ -1363,7 +1375,8 @@ static tng_function_status tng_read_molecules_block static tng_function_status tng_write_molecules_block (tng_trajectory_t tng_data, struct tng_gen_block *block, - write_mode mode) + const tng_write_mode mode, + const tng_hash_mode hash_mode) { int len = 0; int i, j, k, l, offset = 0; @@ -1498,7 +1511,7 @@ static tng_function_status tng_write_molecules_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -1808,7 +1821,7 @@ static tng_function_status tng_write_molecules_block } } - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -1831,7 +1844,8 @@ static tng_function_status tng_write_molecules_block static tng_function_status tng_read_frame_set_block (tng_trajectory_t tng_data, - struct tng_gen_block *block) + struct tng_gen_block *block, + const tng_hash_mode hash_mode) { int i, file_pos, offset = 0; int64_t prev_n_particles; @@ -1873,17 +1887,20 @@ static tng_function_status tng_read_frame_set_block /* FIXME: Does not check if the size of the contents matches the expected * size or if the contents can be read. */ - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + if(hash_mode == TNG_USE_HASH) { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } - if(same_hash != TRUE) - { - printf("Frame set block contents corrupt. Hashes do not match. " - "%s: %d\n", - __FILE__, __LINE__); -// return(TNG_FAILURE); + if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + { + printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); + return(TNG_FAILURE); + } + if(same_hash != TRUE) + { + printf("Frame set block contents corrupt. Hashes do not match. " + "%s: %d\n", + __FILE__, __LINE__); + // return(TNG_FAILURE); + } } file_pos = ftell(tng_data->input_file); @@ -2062,7 +2079,8 @@ static tng_function_status tng_read_frame_set_block static tng_function_status tng_write_frame_set_block (tng_trajectory_t tng_data, struct tng_gen_block *block, - write_mode mode) + const tng_write_mode mode, + const tng_hash_mode hash_mode) { char *temp_name; int64_t i; @@ -2080,7 +2098,7 @@ static tng_function_status tng_write_frame_set_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -2247,7 +2265,7 @@ static tng_function_status tng_write_frame_set_block } offset += sizeof(frame_set->long_stride_prev_frame_set_file_pos); - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -2268,7 +2286,8 @@ static tng_function_status tng_write_frame_set_block static tng_function_status tng_read_trajectory_toc_block (tng_trajectory_t tng_data, - struct tng_gen_block *block) + struct tng_gen_block *block, + const tng_hash_mode hash_mode) { int64_t i, old_n_blocks; int offset = 0, len; @@ -2309,18 +2328,20 @@ static tng_function_status tng_read_trajectory_toc_block /* FIXME: Does not check if the size of the contents matches the expected * size or if the contents can be read. */ - - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + if(hash_mode == TNG_USE_HASH) { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } - if(same_hash != TRUE) - { - printf("Table of contents block contents corrupt. Hashes do not match. " - "%s: %d\n", - __FILE__, __LINE__); -// return(TNG_FAILURE); + if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + { + printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); + return(TNG_FAILURE); + } + if(same_hash != TRUE) + { + printf("Table of contents block contents corrupt. Hashes do not match. " + "%s: %d\n", + __FILE__, __LINE__); + // return(TNG_FAILURE); + } } old_n_blocks = toc->n_blocks; @@ -2383,7 +2404,8 @@ static tng_function_status tng_read_trajectory_toc_block static tng_function_status tng_write_trajectory_toc_block (tng_trajectory_t tng_data, struct tng_gen_block *block, - write_mode mode) + const tng_write_mode mode, + const tng_hash_mode hash_mode) { char *temp_name; int64_t i; @@ -2401,7 +2423,7 @@ static tng_function_status tng_write_trajectory_toc_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -2482,7 +2504,7 @@ static tng_function_status tng_write_trajectory_toc_block } - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -2504,7 +2526,8 @@ static tng_function_status tng_write_trajectory_toc_block static tng_function_status tng_read_trajectory_mapping_block (tng_trajectory_t tng_data, - struct tng_gen_block *block) + struct tng_gen_block *block, + const tng_hash_mode hash_mode) { int64_t i, old_n_particles; int offset = 0; @@ -2547,18 +2570,20 @@ static tng_function_status tng_read_trajectory_mapping_block /* FIXME: Does not check if the size of the contents matches the expected * size or if the contents can be read. */ - - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + if(hash_mode == TNG_USE_HASH) { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } - if(same_hash != TRUE) - { - printf("Particle mapping block contents corrupt. Hashes do not match. " - "%s: %d\n", - __FILE__, __LINE__); -// return(TNG_FAILURE); + if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + { + printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); + return(TNG_FAILURE); + } + if(same_hash != TRUE) + { + printf("Particle mapping block contents corrupt. Hashes do not match. " + "%s: %d\n", + __FILE__, __LINE__); + // return(TNG_FAILURE); + } } frame_set->n_mapping_blocks++; @@ -2646,7 +2671,8 @@ static tng_function_status tng_write_trajectory_mapping_block (tng_trajectory_t tng_data, struct tng_gen_block *block, int mapping_block_nr, - write_mode mode) + const tng_write_mode mode, + const tng_hash_mode hash_mode) { char *temp_name; int i, offset = 0, name_len; @@ -2672,7 +2698,7 @@ static tng_function_status tng_write_trajectory_mapping_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -2773,7 +2799,7 @@ static tng_function_status tng_write_trajectory_mapping_block } - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -3139,7 +3165,8 @@ static tng_function_status tng_write_particle_data_block struct tng_gen_block *block, const int block_index, const struct tng_particle_mapping *mapping, - const write_mode mode) + const tng_write_mode mode, + const tng_hash_mode hash_mode) { int64_t n_particles, num_first_particle, n_frames; int i, j, k, offset = 0, size, len; @@ -3186,7 +3213,7 @@ static tng_function_status tng_write_particle_data_block * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -3490,7 +3517,7 @@ static tng_function_status tng_write_particle_data_block - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -3822,7 +3849,8 @@ static tng_function_status tng_read_data(tng_trajectory_t tng_data, static tng_function_status tng_write_data_block(tng_trajectory_t tng_data, struct tng_gen_block *block, const int block_index, - const write_mode mode) + const tng_write_mode mode, + const tng_hash_mode hash_mode) { int64_t n_frames; int i, j, offset = 0, size, len; @@ -3877,7 +3905,7 @@ static tng_function_status tng_write_data_block(tng_trajectory_t tng_data, * contents are known beforehand (e.g. due to different file versions) */ if(mode == TNG_COPY_EXISTING) { - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -4119,7 +4147,7 @@ static tng_function_status tng_write_data_block(tng_trajectory_t tng_data, } } - if(tng_write_block_header(tng_data, block, mode) != TNG_SUCCESS) + if(tng_write_block_header(tng_data, block, mode, hash_mode) != TNG_SUCCESS) { printf("Cannot write header of file %s. %s: %d\n", tng_data->output_file_path, __FILE__, __LINE__); @@ -4141,7 +4169,8 @@ static tng_function_status tng_write_data_block(tng_trajectory_t tng_data, static tng_function_status tng_read_data_block_contents (tng_trajectory_t tng_data, - struct tng_gen_block *block) + struct tng_gen_block *block, + const tng_hash_mode hash_mode) { int64_t n_values, codec_id, n_frames, first_frame_with_data; int64_t steps_between_data, block_n_particles, first_particle_number; @@ -4183,18 +4212,20 @@ static tng_function_status tng_read_data_block_contents /* FIXME: Does not check if the size of the contents matches the expected * size or if the contents can be read. */ - - if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) - { - printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); - return(TNG_FAILURE); - } - if(same_hash != TRUE) + if(hash_mode == TNG_USE_HASH) { - printf("%s\n", block->hash); - printf("Data block contents corrupt. Hashes do not match. %s: %d\n", - __FILE__, __LINE__); -// return(TNG_FAILURE); + if(tng_verify_hash_match(block, &same_hash) != TNG_SUCCESS) + { + printf("Error comparing hashes. %s: %d\n", __FILE__, __LINE__); + return(TNG_FAILURE); + } + if(same_hash != TRUE) + { + printf("%s\n", block->hash); + printf("Data block contents corrupt. Hashes do not match. %s: %d\n", + __FILE__, __LINE__); + // return(TNG_FAILURE); + } } memcpy(&datatype, block->block_contents+offset, @@ -5924,7 +5955,8 @@ tng_function_status tng_set_signature(tng_trajectory_t tng_data, } tng_function_status tng_read_file_headers(tng_trajectory_t tng_data, - tng_close_file_flag close_file) + tng_close_file_flag close_file, + const tng_hash_mode hash_mode) { int i, cnt = 0, prev_pos = 0; struct tng_gen_block *block = tng_data->non_trajectory_blocks; @@ -5962,7 +5994,7 @@ tng_function_status tng_read_file_headers(tng_trajectory_t tng_data, { // printf("Reading block header %d: %s\n", (int)block->id, block->name); if(tng_read_next_block(tng_data, block, - TNG_KEEP_FILE_OPEN) == TNG_SUCCESS) + TNG_KEEP_FILE_OPEN, hash_mode) == TNG_SUCCESS) { // printf("Read block %s\n", block->name); block++; @@ -5998,7 +6030,8 @@ tng_function_status tng_read_file_headers(tng_trajectory_t tng_data, } tng_function_status tng_write_file_headers(tng_trajectory_t tng_data, - tng_close_file_flag close_file) + tng_close_file_flag close_file, + const tng_hash_mode hash_mode) { int i; struct tng_gen_block *block, data_block; @@ -6016,7 +6049,7 @@ tng_function_status tng_write_file_headers(tng_trajectory_t tng_data, block = &tng_data->non_trajectory_blocks[i]; if(block->id == TNG_GENERAL_INFO) { - if(tng_write_general_info_block(tng_data, block, TNG_NORMAL_WRITE) + if(tng_write_general_info_block(tng_data, block, TNG_NORMAL_WRITE, hash_mode) != TNG_SUCCESS) { printf("Error writing general info block of file %s. %s: %d\n", @@ -6032,7 +6065,7 @@ tng_function_status tng_write_file_headers(tng_trajectory_t tng_data, block = &tng_data->non_trajectory_blocks[i]; if(block->id == TNG_MOLECULES) { - if(tng_write_molecules_block(tng_data, block, TNG_NORMAL_WRITE) + if(tng_write_molecules_block(tng_data, block, TNG_NORMAL_WRITE, hash_mode) != TNG_SUCCESS) { printf("Error writing atom names block of file %s. %s: %d\n", @@ -6050,14 +6083,14 @@ tng_function_status tng_write_file_headers(tng_trajectory_t tng_data, { data_block.id = tng_data->non_tr_data[i].block_id; tng_write_data_block(tng_data, &data_block, - i, TNG_NORMAL_WRITE); + i, TNG_NORMAL_WRITE, hash_mode); } for(i = 0; i < tng_data->n_particle_data_blocks; i++) { data_block.id = tng_data->non_tr_particle_data[i].block_id; tng_write_particle_data_block(tng_data, &data_block, - i, 0, TNG_NORMAL_WRITE); + i, 0, TNG_NORMAL_WRITE, hash_mode); } tng_destroy_block(&data_block); @@ -6074,24 +6107,25 @@ tng_function_status tng_write_file_headers(tng_trajectory_t tng_data, tng_function_status tng_read_next_block(tng_trajectory_t tng_data, struct tng_gen_block *block, - tng_close_file_flag close_file) + const tng_close_file_flag close_file, + const tng_hash_mode hash_mode) { switch(block->id) { case TNG_TRAJECTORY_FRAME_SET: - return(tng_read_frame_set_block(tng_data, block)); + return(tng_read_frame_set_block(tng_data, block, hash_mode)); case TNG_BLOCK_TABLE_OF_CONTENTS: - return(tng_read_trajectory_toc_block(tng_data, block)); + return(tng_read_trajectory_toc_block(tng_data, block, hash_mode)); case TNG_PARTICLE_MAPPING: - return(tng_read_trajectory_mapping_block(tng_data, block)); + return(tng_read_trajectory_mapping_block(tng_data, block, hash_mode)); case TNG_GENERAL_INFO: - return(tng_read_general_info_block(tng_data, block)); + return(tng_read_general_info_block(tng_data, block, hash_mode)); case TNG_MOLECULES: - return(tng_read_molecules_block(tng_data, block)); + return(tng_read_molecules_block(tng_data, block, hash_mode)); default: if(block->id >= TNG_TRAJ_BOX_SHAPE) { - return(tng_read_data_block_contents(tng_data, block)); + return(tng_read_data_block_contents(tng_data, block, hash_mode)); } else { @@ -6169,7 +6203,8 @@ tng_function_status tng_read_next_block(tng_trajectory_t tng_data, // } tng_function_status tng_read_next_frame_set(tng_trajectory_t tng_data, - tng_close_file_flag close_file) + const tng_close_file_flag close_file, + const tng_hash_mode hash_mode) { long int file_pos; struct tng_gen_block block; @@ -6211,7 +6246,8 @@ tng_function_status tng_read_next_frame_set(tng_trajectory_t tng_data, tng_data->current_trajectory_frame_set_input_file_pos = file_pos; if(tng_read_next_block(tng_data, &block, - TNG_KEEP_FILE_OPEN) == TNG_SUCCESS) + TNG_KEEP_FILE_OPEN, + hash_mode) == TNG_SUCCESS) { file_pos = ftell(tng_data->input_file); /* Read all blocks until next frame set block */ @@ -6221,7 +6257,8 @@ tng_function_status tng_read_next_frame_set(tng_trajectory_t tng_data, block.id != TNG_TRAJECTORY_FRAME_SET) { stat = tng_read_next_block(tng_data, &block, - TNG_KEEP_FILE_OPEN) == TNG_SUCCESS; + TNG_KEEP_FILE_OPEN, + hash_mode) == TNG_SUCCESS; if(stat != TNG_CRITICAL) { @@ -6257,7 +6294,8 @@ tng_function_status tng_read_next_frame_set(tng_trajectory_t tng_data, } tng_function_status tng_write_frame_set(tng_trajectory_t tng_data, - tng_close_file_flag close_file) + const tng_close_file_flag close_file, + const tng_hash_mode hash_mode) { int i, j; struct tng_gen_block block; @@ -6281,17 +6319,18 @@ tng_function_status tng_write_frame_set(tng_trajectory_t tng_data, tng_init_block(&block); block.id = TNG_TRAJECTORY_FRAME_SET; - tng_write_frame_set_block(tng_data, &block, TNG_NORMAL_WRITE); + tng_write_frame_set_block(tng_data, &block, TNG_NORMAL_WRITE, hash_mode); if(frame_set->contents.n_blocks > 0) { block.id = TNG_BLOCK_TABLE_OF_CONTENTS; - tng_write_trajectory_toc_block(tng_data, &block, TNG_NORMAL_WRITE); + tng_write_trajectory_toc_block(tng_data, &block, TNG_NORMAL_WRITE, + hash_mode); } for(i = 0; i<frame_set->n_data_blocks; i++) { block.id = frame_set->tr_data[i].block_id; - tng_write_data_block(tng_data, &block, i, TNG_NORMAL_WRITE); + tng_write_data_block(tng_data, &block, i, TNG_NORMAL_WRITE, hash_mode); } if(frame_set->n_mapping_blocks) { @@ -6301,13 +6340,14 @@ tng_function_status tng_write_frame_set(tng_trajectory_t tng_data, if(frame_set->mappings[i].n_particles > 0) { tng_write_trajectory_mapping_block(tng_data, &block, i, - TNG_NORMAL_WRITE); + TNG_NORMAL_WRITE, hash_mode); for(j = 0; j<frame_set->n_particle_data_blocks; j++) { block.id = frame_set->tr_particle_data[i].block_id; tng_write_particle_data_block(tng_data, &block, j, &frame_set->mappings[i], - TNG_NORMAL_WRITE); + TNG_NORMAL_WRITE, + hash_mode); } } } @@ -6318,7 +6358,7 @@ tng_function_status tng_write_frame_set(tng_trajectory_t tng_data, { block.id = frame_set->tr_particle_data[i].block_id; tng_write_particle_data_block(tng_data, &block, - i, 0, TNG_NORMAL_WRITE); + i, 0, TNG_NORMAL_WRITE, hash_mode); } } diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index 9ee49b7..16db334 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -73,7 +73,9 @@ typedef enum {TNG_CONSTANT_N_ATOMS, TNG_VARIABLE_N_ATOMS} tng_variable_n_atoms_f typedef enum {TNG_SUCCESS, TNG_FAILURE, TNG_CRITICAL} tng_function_status; -typedef enum {TNG_NORMAL_WRITE, TNG_COPY_EXISTING} write_mode; +typedef enum {TNG_NORMAL_WRITE, TNG_COPY_EXISTING} tng_write_mode; + +typedef enum {TNG_SKIP_HASH, TNG_USE_HASH} tng_hash_mode; typedef enum {TNG_CHAR_DATA, TNG_INT_DATA, @@ -570,10 +572,13 @@ tng_function_status tng_set_atom_type(tng_trajectory_t tng_data, tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. If close_file == TNG_CLOSE_FILE (1) the input_file will be closed after reading the data. + If hash_mode == TNG_USE_HASH the written md5 hash in the file will be + compared to the md5 hash of the read contents to ensure valid data. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_read_file_headers(tng_trajectory_t tng_data, - tng_close_file_flag close_file); + const tng_close_file_flag close_file, + const tng_hash_mode hash_mode); /* Write the header blocks to the output_file of tng_data. The trajectory blocks must be written separately and iteratively in chunks @@ -581,10 +586,12 @@ tng_function_status tng_read_file_headers(tng_trajectory_t tng_data, tng_data is a trajectory data container. tng_data->output_file_path specifies which file to write to. If the file (output_file) is not open it will be opened. If close_file == TNG_CLOSE_FILE (1) the output_file will be closed after writing the data. + If hash_mode == TNG_USE_HASH an md5 hash for each header block will be generated. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_write_file_headers(tng_trajectory_t tng_data, - tng_close_file_flag close_file); + const tng_close_file_flag close_file, + const tng_hash_mode hash_mode); /* Read one (the next) block (of any kind) from the input_file of tng_data. @@ -594,11 +601,14 @@ tng_function_status tng_write_file_headers(tng_trajectory_t tng_data, data. If block_data->input_file_pos > 0 it is the position from where the reading starts otherwise it starts from the current position. If close_file == TNG_CLOSE_FILE (1) the input_file will be closed after reading the data. + If hash_mode == TNG_USE_HASH the written md5 hash in the file will be + compared to the md5 hash of the read contents to ensure valid data. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_read_next_block(tng_trajectory_t tng_data, struct tng_gen_block *block_data, - tng_close_file_flag close_file); + const tng_close_file_flag close_file, + const tng_hash_mode hash_mode); /* Read one (the next) frame set, including toc, mapping and related data blocks @@ -606,20 +616,25 @@ tng_function_status tng_read_next_block(tng_trajectory_t tng_data, tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. If close_file == TNG_CLOSE_FILE (1) the input_file will be closed after reading the data. + If hash_mode == TNG_USE_HASH the written md5 hash in the file will be + compared to the md5 hash of the read contents to ensure valid data. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_read_next_frame_set(tng_trajectory_t tng_data, - tng_close_file_flag close_file); + const tng_close_file_flag close_file, + const tng_hash_mode hash_mode); /* Write one (the next) frame set, including toc, mapping and related data blocks to the output_file of tng_data. tng_data is a trajectory data container. tng_data->output_file_path specifies which file to write to. If the file (output_file) is not open it will be opened. If close_file == TNG_CLOSE_FILE (1) the output_file will be closed after writing the data. + If hash_mode == TNG_USE_HASH an md5 hash for each block will be generated. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_write_frame_set(tng_trajectory_t tng_data, - tng_close_file_flag close_file); + const tng_close_file_flag close_file, + const tng_hash_mode hash_mode); tng_function_status tng_new_frame_set(tng_trajectory_t tng_data, const int64_t first_frame, @@ -696,7 +711,7 @@ tng_function_status tng_read_frame_set_nr(tng_trajectory_t tng_data, has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_read_frame_nr(tng_trajectory_t tng_data, int64_t frame_nr, - tng_close_file_flag close_file); + const tng_close_file_flag close_file); /* Write one trajectory frame to the output_file of tng_data. tng_data is a trajectory data container. tng_data->output_file_path specifies which @@ -707,7 +722,7 @@ tng_function_status tng_read_frame_nr(tng_trajectory_t tng_data, has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_write_frame_nr(tng_trajectory_t tng_data, int64_t frame_nr, - tng_close_file_flag close_file); + const tng_close_file_flag close_file); /* Read a number of consecutive trajectory frames from the input_file of tng_data. tng_data is a trajectory data container. tng_data->input_file_path specifies which @@ -720,7 +735,7 @@ tng_function_status tng_write_frame_nr(tng_trajectory_t tng_data, tng_function_status tng_read_frame_nrs(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr, - tng_close_file_flag close_file); + const tng_close_file_flag close_file); /* Write a number of consecutive trajectory frames to the output_file of tng_data. tng_data is a trajectory data container. tng_data->output_file_path specifies which @@ -733,7 +748,7 @@ tng_function_status tng_read_frame_nrs(tng_trajectory_t tng_data, tng_function_status tng_write_frame_nrs(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr, - tng_close_file_flag close_file); + const tng_close_file_flag close_file); /* Get the date and time of initial file creation in ISO format (string). tng_data is a trajectory data container. diff --git a/src/tests/tng_io_testing.c b/src/tests/tng_io_testing.c index c9f7e5d..14114f8 100644 --- a/src/tests/tng_io_testing.c +++ b/src/tests/tng_io_testing.c @@ -99,12 +99,12 @@ static tng_function_status tng_test_read_and_write_file { tng_function_status stat; - stat = tng_read_file_headers(traj, TNG_KEEP_FILE_OPEN); + stat = tng_read_file_headers(traj, TNG_KEEP_FILE_OPEN, TNG_USE_HASH); if(stat == TNG_CRITICAL) { return(stat); } - stat = tng_write_file_headers(traj, TNG_KEEP_FILE_OPEN); + stat = tng_write_file_headers(traj, TNG_KEEP_FILE_OPEN, TNG_USE_HASH); if(stat == TNG_CRITICAL) { return(stat); @@ -113,12 +113,12 @@ static tng_function_status tng_test_read_and_write_file while(stat != TNG_CRITICAL && traj->input_file_pos < traj->input_file_len && traj->current_trajectory_frame_set.next_frame_set_file_pos != -1UL) { - stat = tng_read_next_frame_set(traj, TNG_KEEP_FILE_OPEN); + stat = tng_read_next_frame_set(traj, TNG_KEEP_FILE_OPEN, TNG_USE_HASH); if(stat == TNG_CRITICAL) { return(stat); } - stat = tng_write_frame_set(traj, TNG_KEEP_FILE_OPEN); + stat = tng_write_frame_set(traj, TNG_KEEP_FILE_OPEN, TNG_USE_HASH); } return(stat); @@ -148,7 +148,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) return(TNG_CRITICAL); } - if(tng_write_file_headers(traj, TNG_KEEP_FILE_OPEN) == TNG_CRITICAL) + if(tng_write_file_headers(traj, TNG_KEEP_FILE_OPEN, TNG_SKIP_HASH) == TNG_CRITICAL) { return(TNG_CRITICAL); } @@ -227,7 +227,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) free(data); return(TNG_CRITICAL); } - if(tng_write_frame_set(traj, TNG_KEEP_FILE_OPEN) != TNG_SUCCESS) + if(tng_write_frame_set(traj, TNG_KEEP_FILE_OPEN, TNG_SKIP_HASH) != TNG_SUCCESS) { printf("Error writing frame set. %s: %d\n", __FILE__, __LINE__); free(molpos); @@ -248,12 +248,12 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) tng_destroy_trajectory(traj); tng_set_input_file(traj, "/tmp/tng_test.tng"); - stat = tng_read_file_headers(traj, TNG_KEEP_FILE_OPEN); + stat = tng_read_file_headers(traj, TNG_KEEP_FILE_OPEN, TNG_SKIP_HASH); while(stat != TNG_CRITICAL && traj->input_file_pos < traj->input_file_len && traj->current_trajectory_frame_set.next_frame_set_file_pos != -1ULL) { - stat = tng_read_next_frame_set(traj, TNG_KEEP_FILE_OPEN); + stat = tng_read_next_frame_set(traj, TNG_KEEP_FILE_OPEN, TNG_SKIP_HASH); if(stat == TNG_CRITICAL) { return(stat); |