int
strm_var_set(strm_state* state, strm_string name, strm_value val)
{
strm_env *e;
if (!state) {
if (!globals) {
globals = kh_init(env);
}
e = globals;
}
else {
if (!state->env) {
state->env = kh_init(env);
}
e = state->env;
}
return env_set(e, name, val);
}
khash_t(ht) *
mrb_hash_tbl(mrb_state *mrb, mrb_value hash)
{
khash_t(ht) *h = RHASH_TBL(hash);
if (!h) {
RHASH_TBL(hash) = kh_init(ht, mrb);
}
return h;
}
void
mrb_define_method_raw(mrb_state *mrb, struct RClass *c, mrb_sym mid, struct RProc *p)
{
khash_t(mt) *h = c->mt;
khiter_t k;
if (!h) h = c->mt = kh_init(mt, mrb);
k = kh_put(mt, h, mid);
kh_value(h, k) = p;
}
int diffBed(int argc, char * argv[])
{
int help = 0;
char *out = 0;
int n, i;
while ((n = getopt(argc, argv, "o:h")) >= 0)
{
switch(n)
{
case 'o': out = optarg; break;
case 'h': help = 1; break;
default: diffHelp();
}
if (help) diffHelp();
}
n = argc - optind;
if(n < 2) errabort("At least 2 files!");
regHash_t * reghash, * reghash1;
reghash = kh_init(reg);
reghash1 = kh_init(reg);
int ret = 0;
bedHand->read(argv[optind], (void *)reghash, 0, 0, &ret);
bedHand->merge(reghash);
for (i = 1; i < n; ++i)
{
bedHand->read(argv[optind+i], (void *)reghash1, 0, 0, &ret);
}
bedHand->merge(reghash1);
bedHand->diff(reghash, reghash1);
inf_t * inf = bedHand->stat(reghash);
if (ret)
{
warnings("the input bed file might not be standard bed format 0-based, please make sure the input files is in same base system"
"you can use '1to0' to trans the base systems first");
}
writeout("There are %d bp in the first file but not in others.\n", inf->length);
freemem(inf);
bedHand->destroy(reghash1, destroy_void);
if (out) bedHand->save(out, reghash);
bedHand->destroy(reghash, destroy_void);
return 1;
}
mrb_value
mrb_hash_new_capa(mrb_state *mrb, size_t capa)
{
struct RHash *h;
h = (struct RHash*)mrb_obj_alloc(mrb, MRB_TT_HASH, mrb->hash_class);
h->ht = kh_init(ht, mrb);
kh_resize(ht, h->ht, capa);
h->iv = 0;
return mrb_obj_value(h);
}
void parg_asset_onload(const char* name, parg_buffer* buf)
{
parg_token id = parg_token_from_string(name);
parg_assert(buf, "Unable to load asset");
if (!_asset_registry) {
_asset_registry = kh_init(assmap);
}
int ret;
int iter = kh_put(assmap, _asset_registry, id, &ret);
kh_value(_asset_registry, iter) = buf;
}
static struct RClass*
boot_defclass(mrb_state *mrb, struct RClass *super)
{
struct RClass *c;
c = (struct RClass*)mrb_obj_alloc(mrb, MRB_TT_CLASS, mrb->class_class);
c->super = super ? super : mrb->object_class;
mrb_field_write_barrier(mrb, (struct RBasic*)c, (struct RBasic*)super);
c->mt = kh_init(mt, mrb);
return c;
}
pic_value
pic_make_weak(pic_state *pic)
{
struct weak *weak;
weak = (struct weak *)pic_obj_alloc(pic, sizeof(struct weak), PIC_TYPE_WEAK);
weak->prev = NULL;
kh_init(weak, &weak->hash);
return pic_obj_value(weak);
}
/** Create an attack vector object
*
* @param corsaro The corsaro object associated with the vector
* @return an empty attack vector object
*/
static attack_vector_t *attack_vector_init(corsaro_t *corsaro)
{
attack_vector_t *av = NULL;
if((av = malloc_zero(sizeof(attack_vector_t))) == NULL)
{
corsaro_log(__func__, corsaro, "could not malloc memory for attack vector");
return NULL;
}
av->attack_ip_hash = kh_init(32xx);
assert(av->attack_ip_hash != NULL);
av->attack_port_hash = kh_init(32xx);
assert(av->attack_port_hash != NULL);
av->target_port_hash = kh_init(32xx);
assert(av->target_port_hash != NULL);
return av;
}
/** Implements the init_output function of the plugin API */
int bgpcorsaro_pfxmonitor_init_output(bgpcorsaro_t *bgpcorsaro)
{
struct bgpcorsaro_pfxmonitor_state_t *state;
bgpcorsaro_plugin_t *plugin = PLUGIN(bgpcorsaro);
assert(plugin != NULL);
if ((state = malloc_zero(sizeof(struct bgpcorsaro_pfxmonitor_state_t))) ==
NULL) {
bgpcorsaro_log(__func__, bgpcorsaro,
"could not malloc bgpcorsaro_pfxmonitor_state_t");
goto err;
}
bgpcorsaro_plugin_register_state(bgpcorsaro->plugin_manager, plugin, state);
/* initialize state with default values */
state = STATE(bgpcorsaro);
strncpy(state->metric_prefix, PFXMONITOR_DEFAULT_METRIC_PFX,
PFXMONITOR_METRIC_PFX_LEN);
strncpy(state->ip_space_name, PFXMONITOR_DEFAULT_IPSPACE_NAME,
PFXMONITOR_METRIC_PFX_LEN);
if ((state->poi = bgpstream_ip_counter_create()) == NULL) {
goto err;
}
state->peer_asns_th = PFXMONITOR_DEFAULT_PEER_ASNS_THRESHOLD;
state->more_specific = 0;
/* parse the arguments */
if (parse_args(bgpcorsaro) != 0) {
goto err;
}
graphite_safe(state->metric_prefix);
graphite_safe(state->ip_space_name);
/* create all the sets and maps we need */
if ((state->overlapping_pfx_cache = bgpstream_pfx_storage_set_create()) ==
NULL ||
(state->non_overlapping_pfx_cache = bgpstream_pfx_storage_set_create()) ==
NULL ||
(state->pfx_info = kh_init(pfx_info_map)) == NULL ||
(state->unique_origins = bgpstream_id_set_create()) == NULL ||
(state->peer_asns = bgpstream_id_set_create()) == NULL) {
goto err;
}
/* defer opening the output file until we start the first interval */
return 0;
err:
bgpcorsaro_pfxmonitor_close_output(bgpcorsaro);
return -1;
}
void
mrb_define_method_vm(mrb_state *mrb, struct RClass *c, mrb_sym name, mrb_value body)
{
khash_t(mt) *h = c->mt;
khiter_t k;
int ret;
if (!h) h = c->mt = kh_init(mt, mrb);
k = kh_put(mt, h, name, &ret);
kh_value(h, k) = mrb_proc_ptr(body);
}
void hw_http_add_route(char *route, http_request_callback callback)
{
if (routes == NULL)
{
/* routes = rxt_init(); */
routes = kh_init(string_hashmap);
}
/* rxt_put(route, callback, routes); */
set_route(routes, route, callback);
printf("Added route %s\n", route); // TODO: Replace with logging instead.
}
struct pic_reg *
pic_make_reg(pic_state *pic)
{
struct pic_reg *reg;
reg = (struct pic_reg *)pic_obj_alloc(pic, sizeof(struct pic_reg), PIC_TT_REG);
reg->prev = NULL;
kh_init(reg, ®->hash);
return reg;
}
static BGZF *bgzf_read_init(void)
{
BGZF *fp;
fp = calloc(1, sizeof(BGZF));
fp->uncompressed_block_size = MAX_BLOCK_SIZE;
fp->uncompressed_block = malloc(MAX_BLOCK_SIZE);
fp->compressed_block_size = MAX_BLOCK_SIZE;
fp->compressed_block = malloc(MAX_BLOCK_SIZE);
fp->cache_size = 0;
fp->cache = kh_init(cache);
return fp;
}
struct RClass*
mrb_define_module_id(mrb_state *mrb, mrb_sym name)
{
struct RClass *m = mrb_module_new(mrb);
m->mt = kh_init(mt, mrb);
mrb_obj_iv_set(mrb, (struct RObject*)mrb->object_class,
name, mrb_obj_value(m));
mrb_name_class(mrb, m, name);
return m;
}
int main(int argc, char *argv[]) {
char* person_input_file = makepath(argv[1], "person", "csv");
char* interest_input_file = makepath(argv[1], "interest", "csv");
char* knows_input_file = makepath(argv[1], "knows", "csv");
char* person_output_file = makepath(argv[2], "person", "bin");
char* interest_output_file = makepath(argv[2], "interest", "bin");
char* knows_output_file = makepath(argv[2], "knows", "bin");
khiter_t k;
int person_map_fd;
struct stat st;
if (argc < 3) {
fprintf(stderr, "Usage: [csv input path] [output path]\n");
exit(-1);
}
if (stat(argv[2], &st) == -1) {
if (mkdir(argv[2], 0700) != 0) {
fprintf(stderr, "Unable to create output directory %s\n", argv[2]);
exit(-1);
}
}
// first pass person, parse person, write to binary and store bin offset in hash table
person_offsets = kh_init(pht);
person = malloc(sizeof(Person));
person->interest_n = person->knows_n = 0;
person_out = open_binout(person_output_file);
parse_csv(person_input_file, &person_line_handler);
// mmap person.bin binary file for updates
fclose(person_out);
person_map_fd = open(person_output_file, O_RDWR);
person_map = (Person *) mmap(0, person_offset * sizeof(Person), PROT_READ | PROT_WRITE,
MAP_SHARED, person_map_fd, 0);
if (person_map_fd == 0 || person_map == MAP_FAILED) {
fprintf(stderr, "Failed to map person binary.\n");
exit(-1);
}
close(person_map_fd);
// pass through interest and friends, write to binary, set offsets in person
person_id = 0;
interest_out = open_binout(interest_output_file);
parse_csv(interest_input_file, &interest_line_handler);
person_id = 0;
knows_out = open_binout(knows_output_file);
parse_csv(knows_input_file, &knows_line_handler);
return 0;
}
static BGZF *bgzf_read_init()
{
BGZF *fp;
fp = calloc(1, sizeof(BGZF));
fp->is_write = 0;
fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
#ifdef BGZF_CACHE
fp->cache = kh_init(cache);
#endif
return fp;
}
ForwardIndex *NewForwardIndex(Document doc) {
ForwardIndex *idx = malloc(sizeof(ForwardIndex));
idx->hits = kh_init(32);
idx->docScore = doc.score;
idx->docId = doc.docId;
idx->totalFreq = 0;
idx->maxFreq = 0;
idx->stemmer = NewStemmer(SnowballStemmer, doc.language);
return idx;
}
khash_s2i *hash_s2i_create(void) {
khash_s2i *h = calloc(1, sizeof(*h));
if (!h)
return NULL;
h->h = kh_init(s2i);
if (!h->h) {
free(h);
return NULL;
}
return h;
}
void *bcf_build_refhash(bcf_hdr_t *h)
{
khash_t(str2id) *hash;
int i, ret;
hash = kh_init(str2id);
for (i = 0; i < h->n_ref; ++i) {
khint_t k;
k = kh_put(str2id, hash, h->ns[i], &ret); // FIXME: check ret
kh_val(hash, k) = i;
}
return hash;
}
hash_t *
hash_new() {
hash_t *hash;
hash = malloc(sizeof(hash_t));
hash->table = kh_init(str);
pthread_mutex_init(&hash->mutex, NULL);
return hash;
}
int trimBed(int argc, char *argv[])
{
int help = 0;
int n;
int i;
char *out = 0;
int trim1 = 0;
int trim2 = 0;
while ((n = getopt(argc, argv, "o:r:l:h")) >= 0)
{
switch(n)
{
case 'o' : out = optarg; break;
case 'l' : trim1 = atoi(optarg); break;
case 'r' : trim2 = atoi(optarg); break;
case 'h' : help = 1; break;
default :
errabort("%c : unknown option!", (char)n);
break;
}
if (help) trimHelp();
}
if (trim1 == 0 && trim2 == 0) errabort("You must set a trim size!");
if (trim1 < 0 || trim2 < 0) errabort("Trim size must be a postive int!");
n = argc - optind;
if (n < 1) errabort("Sucker! Set the bed file(s)!");
regHash_t *rghsh = kh_init(reg);
int ret = 0;
for (i = 0; i < n; ++i)
{
bedHand->read(argv[optind+i], rghsh, 0, 0, &ret);
}
bedHand->merge(rghsh);
if (ret)
{
warnings("the input bed file might not be standard bed format 0-based, please make sure the input files is in same base system"
"you can use '1to0' to trans the base systems first");
}
inf_t *itmp = bedHand->stat(rghsh);
bedHand->trim(rghsh, trim1, trim2);
inf_t *inf = bedHand->stat(rghsh);
if (out) bedHand->save(out, rghsh);
unsigned trim_length = itmp->length - inf->length;
writeout("Trimmed %d bp\n"
"The length of whole regions is %d bp\n"
,trim_length, inf->length);
freemem(itmp);
freemem(inf);
bedHand->destroy(rghsh, destroy_void);
return 1;
}
/* program-wide initialization of sample information */
void bam_sample_info_init(const char *samples_file,
const char *sample_pairs_file)
{
khash_t(remap_h) *sample_map = kh_init(remap_h);
init_sample_attributes(samples_file, sample_map);
init_sample_pairs(sample_pairs_file, sample_map);
khiter_t k;
for (k = kh_begin(sample_map); k != kh_end(sample_map); ++k)
if (kh_exist(sample_map, k))
free((char *)kh_key(sample_map, k));
kh_destroy(remap_h, sample_map);
}
PyMODINIT_FUNC
PyInit_pyext(void){
PyObject *mod;
mod = PyModule_Create(&pyext_module);
if(mod == NULL){
return NULL;
}
pyep_ht = kh_init(ptr);
return mod;
}
void
mrb_define_method_raw(mrb_state *mrb, struct RClass *c, mrb_sym mid, struct RProc *p)
{
khash_t(mt) *h = c->mt;
khiter_t k;
if (!h) h = c->mt = kh_init(mt, mrb);
k = kh_put(mt, h, mid);
kh_value(h, k) = p;
if (p) {
mrb_field_write_barrier(mrb, (struct RBasic *)c, (struct RBasic *)p);
}
}
void hw_http_add_route(char *route, http_request_callback callback, void* user_data)
{
hw_route_entry* route_entry = malloc(sizeof(hw_route_entry));
route_entry->callback = callback;
route_entry->user_data = user_data;
if (routes == NULL)
{
routes = kh_init(string_hashmap);
}
set_route(routes, route, route_entry);
printf("Added route %s\n", route); // TODO: Replace with logging instead.
}
void bgpstream_filter_mgr_rib_period_filter_add(
bgpstream_filter_mgr_t *bs_filter_mgr, uint32_t period)
{
bgpstream_debug("\tBSF_MGR:: add_filter start");
assert(bs_filter_mgr != NULL);
if (period != 0 && bs_filter_mgr->last_processed_ts == NULL) {
if ((bs_filter_mgr->last_processed_ts = kh_init(collector_ts)) == NULL) {
bgpstream_log_warn(
"\tBSF_MGR: can't allocate memory for collectortype map");
}
}
bs_filter_mgr->rib_period = period;
bgpstream_debug("\tBSF_MGR:: add_filter end");
}
static void load_hfile_plugins()
{
static const struct hFILE_scheme_handler
data = { hopen_mem, hfile_always_local, "built-in", 80 },
file = { hopen_fd_fileuri, hfile_always_local, "built-in", 80 },
preload = { hopen_preload, is_preload_url_remote, "built-in", 80 };
schemes = kh_init(scheme_string);
if (schemes == NULL) abort();
hfile_add_scheme_handler("data", &data);
hfile_add_scheme_handler("file", &file);
hfile_add_scheme_handler("preload", &preload);
init_add_plugin(NULL, hfile_plugin_init_net, "knetfile");
init_add_plugin(NULL, hfile_plugin_init_mem, "mem");
#ifdef ENABLE_PLUGINS
struct hts_path_itr path;
const char *pluginname;
hts_path_itr_setup(&path, NULL, NULL, "hfile_", 6, NULL, 0);
while ((pluginname = hts_path_itr_next(&path)) != NULL) {
void *obj;
int (*init)(struct hFILE_plugin *) = (int (*)(struct hFILE_plugin *))
load_plugin(&obj, pluginname, "hfile_plugin_init");
if (init) {
if (init_add_plugin(obj, init, pluginname) != 0)
close_plugin(obj);
}
}
#else
#ifdef HAVE_LIBCURL
init_add_plugin(NULL, hfile_plugin_init_libcurl, "libcurl");
#endif
#ifdef ENABLE_GCS
init_add_plugin(NULL, hfile_plugin_init_gcs, "gcs");
#endif
#ifdef ENABLE_S3
init_add_plugin(NULL, hfile_plugin_init_s3, "s3");
#endif
#endif
// In the unlikely event atexit() fails, it's better to succeed here and
// carry on; then eventually when the program exits, we'll merely close
// down the plugins uncleanly, as if we had aborted.
(void) atexit(hfile_exit);
}
/** Create a new memoization data container structure and return a pointer to it
@param[in] numContexts: Number of memoization contexts to store.
@return: A new memoization data container, for storing and retreiving function calls by context
*/
MEMOIZATION_DATA_CONTAINER* newMemoizationContainer(unsigned int numContexts){
unsigned int i;
MEMOIZATION_DATA_CONTAINER* container = malloc(sizeof(MEMOIZATION_DATA_CONTAINER));
container->numContexts = numContexts;
container->contexts = calloc(numContexts, sizeof(khash_t(MEMO_CACHE)*));
container->isContextEnabled = calloc(numContexts, sizeof(int));
container->isCacheDirty = calloc(numContexts, sizeof(int));
for (i=0; i<numContexts; i++){
// All caches initially inactive by default.
container->isContextEnabled[i] = 0;
container->isCacheDirty[i] = 0;
container->contexts[i] = kh_init(MEMO_CACHE);
}
return container;
}
void
mrb_define_method_vm(mrb_state *mrb, struct RClass *c, mrb_sym name, mrb_value body)
{
khash_t(mt) *h = c->mt;
khiter_t k;
struct RProc *p;
if (!h) h = c->mt = kh_init(mt, mrb);
k = kh_put(mt, h, name);
p = mrb_proc_ptr(body);
kh_value(h, k) = p;
if (p) {
mrb_field_write_barrier(mrb, (struct RBasic *)c, (struct RBasic *)p);
}
}
