static void initialize_output_data_structures(shared_options_data_t *shared_options, list_t **output_list, cp_hashtable **summary_count, cp_hashtable **gene_list) {
// Initialize output text list
*output_list = (list_t*) malloc (sizeof(list_t));
list_init("output", shared_options->num_threads, shared_options->max_batches * shared_options->batch_lines, *output_list);
// Initialize summary counters and genes list
*summary_count = cp_hashtable_create_by_option(COLLECTION_MODE_DEEP,
64,
cp_hash_istring,
(cp_compare_fn) strcasecmp,
NULL,
(cp_destructor_fn) free_file_key2,
NULL,
(cp_destructor_fn) free_summary_counter
);
*gene_list = cp_hashtable_create_by_option(COLLECTION_MODE_DEEP,
64,
cp_hash_istring,
(cp_compare_fn) strcasecmp,
NULL,
(cp_destructor_fn) free_file_key2,
NULL,
NULL
);
}
static int initialize_output_files(char *output_directory, size_t output_directory_len, cp_hashtable **output_files) {
// Initialize collections of file descriptors
*output_files = cp_hashtable_create_by_option(COLLECTION_MODE_DEEP,
50,
cp_hash_int,
(cp_compare_fn) int_cmp,
NULL,
(cp_destructor_fn) free_file_key1,
NULL,
(cp_destructor_fn) free_file_descriptor
);
char all_variants_filename[output_directory_len + 18];
sprintf(all_variants_filename, "%s/all_variants.txt", output_directory);
FILE *all_variants_file = fopen(all_variants_filename, "a");
if (!all_variants_file) { // Can't store results
return 1;
}
char *key = (char*) calloc (13, sizeof(char));
strncat(key, "all_variants", 12);
cp_hashtable_put(*output_files, key, all_variants_file);
char summary_filename[output_directory_len + 13];
sprintf(summary_filename, "%s/summary.txt", output_directory);
FILE *summary_file = fopen(summary_filename, "a");
if (!summary_file) { // Can't store results
return 2;
}
key = (char*) calloc (8, sizeof(char));
strncat(key, "summary", 7);
cp_hashtable_put(*output_files, key, summary_file);
char snp_phenotype_filename[output_directory_len + 20];
sprintf(snp_phenotype_filename, "%s/snp_phenotypes.txt", output_directory);
FILE *snp_phenotype_file = fopen(snp_phenotype_filename, "a");
if (!snp_phenotype_filename) {
return 3;
}
key = (char*) calloc (15, sizeof(char));
strncat(key, "snp_phenotypes", 14);
cp_hashtable_put(*output_files, key, snp_phenotype_file);
char mutation_phenotype_filename[output_directory_len + 25];
sprintf(mutation_phenotype_filename, "%s/mutation_phenotypes.txt", output_directory);
FILE *mutation_phenotype_file = fopen(mutation_phenotype_filename, "a");
if (!mutation_phenotype_filename) {
return 3;
}
key = (char*) calloc (20, sizeof(char));
strncat(key, "mutation_phenotypes", 19);
cp_hashtable_put(*output_files, key, mutation_phenotype_file);
return 0;
}
int load_mime_types(char *filename)
{
FILE *fp;
char mimebuf[LINELEN];
int rc = 0;
char *name;
char *ext;
char *curr;
mimemap =
cp_hashtable_create_by_option(COLLECTION_MODE_NOSYNC |
COLLECTION_MODE_COPY |
COLLECTION_MODE_DEEP,
500,
cp_hash_string,
cp_hash_compare_string,
(cp_copy_fn) strdup,
(cp_destructor_fn) free,
(cp_copy_fn) strdup,
(cp_destructor_fn) free);
fp = fopen(filename, "r");
if (fp == NULL)
{
cp_error(CP_INVALID_VALUE, "can\'t open %s", filename);
cp_hashtable_destroy(mimemap);
return -1;
}
while (fgets(mimebuf, LINELEN, fp))
{
if (mimebuf[0] == '#') continue;
name = curr = mimebuf;
while (*curr && !isspace(*curr)) curr++;
if (*curr == '\0') continue; /* no extension for this type */
*curr++ = '\0';
while (1)
{
while (*curr && isspace(*curr)) curr++;
ext = curr;
while (*curr && !isspace(*curr)) curr++;
if (strlen(ext))
{
*curr++ = '\0';
cp_hashtable_put(mimemap, ext, name);
}
else
break;
}
}
fclose(fp);
return rc;
}
int cp_log_init(char *filename, int verbosity)
{
int i, err_code_count;
unsigned long thread_no;
#ifdef SIGHUP
struct sigaction act;
#endif
log_filename = strdup(filename);
logfile = fopen(filename, "a+");
if (logfile == NULL)
return CP_LOG_FILE_OPEN_FAILURE;
loglevel = verbosity;
err_code_count = sizeof(error_messages) / sizeof(error_code_legend);
error_message_lookup =
cp_hashtable_create_by_mode(COLLECTION_MODE_NOSYNC,
err_code_count * 2,
cp_hash_int,
cp_hash_compare_int);
for (i = 0; i < err_code_count; i++)
{
error_code_legend *entry = &error_messages[i];
cp_hashtable_put(error_message_lookup, &entry->code, entry->msg);
}
thread_id =
cp_hashtable_create_by_option(COLLECTION_MODE_DEEP, 10,
cp_hash_long, cp_hash_compare_long,
NULL, free, NULL, free);
thread_count = 0;
// thread_no = (unsigned long) pthread_self();
thread_no = (unsigned long) cp_thread_self();
get_thread_serial(thread_no); /* establish this as thread number one */
log_closing = 0;
#ifdef SIGHUP
act.sa_handler = cp_log_default_signal_handler;
sigemptyset(&act.sa_mask);
act.sa_flags = 0;
sigaction(SIGHUP, &act, NULL);
#endif
// signal(SIGHUP, cp_log_default_signal_handler);
return 0;
}
int initialize_ws_output(shared_options_data_t *shared_options, effect_options_data_t *options_data){
int num_threads = shared_options->num_threads;
char *outdir = shared_options->output_directory;
// Initialize output text list
output_list = (list_t*) malloc (sizeof(list_t));
list_init("output", num_threads, shared_options->max_batches * shared_options->batch_lines, output_list);
// Initialize collections of file descriptors
output_files = cp_hashtable_create_by_option(COLLECTION_MODE_DEEP,
50,
cp_hash_int,
(cp_compare_fn) int_cmp,
NULL,
(cp_destructor_fn) free_file_key1,
NULL,
(cp_destructor_fn) free_file_descriptor
);
char all_variants_filename[strlen(outdir) + 18];
sprintf(all_variants_filename, "%s/all_variants.txt", outdir);
all_variants_file = fopen(all_variants_filename, "a");
if (!all_variants_file) { // Can't store results
return 1;
}
char *key = (char*) calloc (13, sizeof(char));
strncat(key, "all_variants", 12);
cp_hashtable_put(output_files, key, all_variants_file);
char summary_filename[strlen(outdir) + 13];
sprintf(summary_filename, "%s/summary.txt", outdir);
summary_file = fopen(summary_filename, "a");
if (!summary_file) { // Can't store results
return 2;
}
key = (char*) calloc (8, sizeof(char));
strncat(key, "summary", 7);
cp_hashtable_put(output_files, key, summary_file);
char snp_phenotype_filename[strlen(outdir) + 20];
sprintf(snp_phenotype_filename, "%s/snp_phenotypes.txt", outdir);
snp_phenotype_file = fopen(snp_phenotype_filename, "a");
if (!snp_phenotype_filename) {
return 3;
}
key = (char*) calloc (15, sizeof(char));
strncat(key, "snp_phenotypes", 14);
cp_hashtable_put(output_files, key, snp_phenotype_file);
char mutation_phenotype_filename[strlen(outdir) + 25];
sprintf(mutation_phenotype_filename, "%s/mutation_phenotypes.txt", outdir);
mutation_phenotype_file = fopen(mutation_phenotype_filename, "a");
if (!mutation_phenotype_filename) {
return 3;
}
key = (char*) calloc (20, sizeof(char));
strncat(key, "mutation_phenotypes", 19);
cp_hashtable_put(output_files, key, mutation_phenotype_file);
// Initialize summary counters and genes list
summary_count = cp_hashtable_create_by_option(COLLECTION_MODE_DEEP,
64,
cp_hash_istring,
(cp_compare_fn) strcasecmp,
NULL,
(cp_destructor_fn) free_file_key2,
NULL,
(cp_destructor_fn) free_summary_counter
);
gene_list = cp_hashtable_create_by_option(COLLECTION_MODE_DEEP,
64,
cp_hash_istring,
(cp_compare_fn) strcasecmp,
NULL,
(cp_destructor_fn) free_file_key2,
NULL,
NULL
);
// Create a buffer for each thread
line = (char**) calloc (num_threads, sizeof(char*));
output_line = (char**) calloc (num_threads, sizeof(char*));
max_line_size = (int*) calloc (num_threads, sizeof(int));
snp_line = (char**) calloc (num_threads, sizeof(char*));
snp_output_line = (char**) calloc (num_threads, sizeof(char*));
snp_max_line_size = (int*) calloc (num_threads, sizeof(int));
mutation_line = (char**) calloc (num_threads, sizeof(char*));
mutation_output_line = (char**) calloc (num_threads, sizeof(char*));
mutation_max_line_size = (int*) calloc (num_threads, sizeof(int));
for (int i = 0; i < num_threads; i++) {
max_line_size[i] = snp_max_line_size[i] = mutation_max_line_size[i] = 512;
line[i] = (char*) calloc (max_line_size[i], sizeof(char));
output_line[i] = (char*) calloc (max_line_size[i], sizeof(char));
snp_line[i] = (char*) calloc (snp_max_line_size[i], sizeof(char));
snp_output_line[i] = (char*) calloc (snp_max_line_size[i], sizeof(char));
mutation_line[i] = (char*) calloc (mutation_max_line_size[i], sizeof(char));
mutation_output_line[i] = (char*) calloc (mutation_max_line_size[i], sizeof(char));
}
return 0;
}
