int main() { hattrie_t* T = hattrie_create(); const size_t n = 1000000; // how many strings const size_t m_low = 50; // minimum length of each string const size_t m_high = 500; // maximum length of each string char x[501]; size_t i, m; for (i = 0; i < n; ++i) { m = m_low + rand() % (m_high - m_low); randstr(x, m); *hattrie_get(T, x, m) = 1; } hattrie_iter_t* it; clock_t t0, t; const size_t repetitions = 100; size_t r; /* iterate in unsorted order */ fprintf(stderr, "iterating out of order ... "); t0 = clock(); for (r = 0; r < repetitions; ++r) { it = hattrie_iter_begin(T, false); while (!hattrie_iter_finished(it)) { hattrie_iter_next(it); } hattrie_iter_free(it); } t = clock(); fprintf(stderr, "finished. (%0.2f seconds)\n", (double) (t - t0) / (double) CLOCKS_PER_SEC); /* iterate in sorted order */ fprintf(stderr, "iterating in order ... "); t0 = clock(); for (r = 0; r < repetitions; ++r) { it = hattrie_iter_begin(T, true); while (!hattrie_iter_finished(it)) { hattrie_iter_next(it); } hattrie_iter_free(it); } t = clock(); fprintf(stderr, "finished. (%0.2f seconds)\n", (double) (t - t0) / (double) CLOCKS_PER_SEC); hattrie_free(T); return 0; }
const char* hattrie_iter_key(hattrie_iter_t* i, size_t* len) { if (hattrie_iter_finished(i)) return NULL; uint16_t sublen; const char* subkey; if (i->has_nil_key) { subkey = NULL; sublen = 0; } else subkey = hhash_iter_key(i->i, &sublen); if (i->keysize < i->level + sublen + 1) { while (i->keysize < i->level + sublen + 1) i->keysize *= 2; i->key = realloc(i->key, i->keysize * sizeof(char)); } if (sublen > 0) { memcpy(i->key + i->level, subkey, sublen); } i->key[i->level + sublen] = '\0'; *len = i->level + sublen; return i->key; }
static int recreate_nsec3_tree(const zone_contents_t *z, zone_contents_t *out) { out->nsec3_nodes = hattrie_dup(z->nsec3_nodes, NULL); if (out->nsec3_nodes == NULL) { return KNOT_ENOMEM; } hattrie_iter_t *itt = hattrie_iter_begin(z->nsec3_nodes, false); if (itt == NULL) { return KNOT_ENOMEM; } while (!hattrie_iter_finished(itt)) { const zone_node_t *to_cpy = (zone_node_t *)*hattrie_iter_val(itt); zone_node_t *to_add = node_shallow_copy(to_cpy, NULL); if (to_add == NULL) { hattrie_iter_free(itt); return KNOT_ENOMEM; } int ret = zone_contents_add_nsec3_node(out, to_add); if (ret != KNOT_EOK) { hattrie_iter_free(itt); node_free(&to_add, NULL); return ret; } hattrie_iter_next(itt); } hattrie_iter_free(itt); hattrie_build_index(out->nsec3_nodes); return KNOT_EOK; }
void hattrie_iter_next(hattrie_iter_t* i) { if (hattrie_iter_finished(i)) return; if (i->i != NULL && !ahtable_iter_finished(i->i)) { ahtable_iter_next(i->i); } else if (i->has_nil_key) { i->has_nil_key = false; i->nil_val = 0; hattrie_iter_nextnode(i); } while (((i->i == NULL || ahtable_iter_finished(i->i)) && !i->has_nil_key) && i->stack != NULL ) { ahtable_iter_free(i->i); i->i = NULL; hattrie_iter_nextnode(i); } if (i->i != NULL && ahtable_iter_finished(i->i)) { ahtable_iter_free(i->i); i->i = NULL; } }
static int axfr_process_node_tree(knot_pkt_t *pkt, const void *item, struct xfr_proc *state) { assert(item != NULL); struct axfr_proc *axfr = (struct axfr_proc*)state; if (axfr->i == NULL) { axfr->i = hattrie_iter_begin(item, true); } /* Put responses. */ int ret = KNOT_EOK; zone_node_t *node = NULL; while (!hattrie_iter_finished(axfr->i)) { node = (zone_node_t *)*hattrie_iter_val(axfr->i); ret = axfr_put_rrsets(pkt, node, axfr); if (ret != KNOT_EOK) { break; } hattrie_iter_next(axfr->i); } /* Finished all nodes. */ if (ret == KNOT_EOK) { hattrie_iter_free(axfr->i); axfr->i = NULL; } return ret; }
int zone_tree_apply_inorder(zone_tree_t *tree, zone_tree_apply_cb_t function, void *data) { if (function == NULL) { return KNOT_EINVAL; } if (zone_tree_is_empty(tree)) { return KNOT_EOK; } int result = KNOT_EOK; hattrie_iter_t *i = hattrie_iter_begin(tree, 1); while(!hattrie_iter_finished(i)) { result = function((zone_node_t **)hattrie_iter_val(i), data); if (result != KNOT_EOK) { break; } hattrie_iter_next(i); } hattrie_iter_free(i); return result; }
/*! * \brief Call a function for each piece of the chain formed by sorted nodes. */ int knot_nsec_chain_iterate_create(knot_zone_tree_t *nodes, chain_iterate_create_cb callback, nsec_chain_iterate_data_t *data) { assert(nodes); assert(callback); bool sorted = true; hattrie_iter_t *it = hattrie_iter_begin(nodes, sorted); if (!it) { return KNOT_ENOMEM; } if (hattrie_iter_finished(it)) { hattrie_iter_free(it); return KNOT_EINVAL; } zone_node_t *first = (zone_node_t *)*hattrie_iter_val(it); zone_node_t *previous = first; zone_node_t *current = first; hattrie_iter_next(it); int result = KNOT_EOK; while (!hattrie_iter_finished(it)) { current = (zone_node_t *)*hattrie_iter_val(it); result = callback(previous, current, data); if (result == NSEC_NODE_SKIP) { // No NSEC should be created for 'current' node, skip ; } else if (result == KNOT_EOK) { previous = current; } else { hattrie_iter_free(it); return result; } hattrie_iter_next(it); } hattrie_iter_free(it); return result == NSEC_NODE_SKIP ? callback(previous, first, data) : callback(current, first, data); }
value_t* hattrie_iter_val(hattrie_iter_t* i) { if (i->has_nil_key) return &i->nil_val; if (hattrie_iter_finished(i)) return NULL; return ahtable_iter_val(i->i); }
static int recreate_normal_tree(const zone_contents_t *z, zone_contents_t *out) { out->nodes = hattrie_dup(z->nodes, NULL); if (out->nodes == NULL) { return KNOT_ENOMEM; } // Insert APEX first. zone_node_t *apex_cpy = node_shallow_copy(z->apex, NULL); if (apex_cpy == NULL) { return KNOT_ENOMEM; } // Normal additions need apex ... so we need to insert directly. int ret = zone_tree_insert(out->nodes, apex_cpy); if (ret != KNOT_EOK) { node_free(&apex_cpy, NULL); return ret; } out->apex = apex_cpy; hattrie_iter_t *itt = hattrie_iter_begin(z->nodes, true); if (itt == NULL) { return KNOT_ENOMEM; } while (!hattrie_iter_finished(itt)) { const zone_node_t *to_cpy = (zone_node_t *)*hattrie_iter_val(itt); if (to_cpy == z->apex) { // Inserted already. hattrie_iter_next(itt); continue; } zone_node_t *to_add = node_shallow_copy(to_cpy, NULL); if (to_add == NULL) { hattrie_iter_free(itt); return KNOT_ENOMEM; } int ret = zone_contents_add_node(out, to_add, true); if (ret != KNOT_EOK) { node_free(&to_add, NULL); hattrie_iter_free(itt); return ret; } hattrie_iter_next(itt); } hattrie_iter_free(itt); hattrie_build_index(out->nodes); return KNOT_EOK; }
void test_hattrie_find_prev() { fprintf(stderr, "finding previous for %zu keys ... \n", k); hattrie_build_index(T); hattrie_iter_t* i = hattrie_iter_begin(T, true); value_t* u; const char *key = NULL; char *dkey = NULL; char *fkey = NULL; size_t len = 0, flen = 0; while (!hattrie_iter_finished(i)) { u = hattrie_iter_val(i); key = hattrie_iter_key(i, &len); /* first key */ if (!fkey) { fkey = malloc(len); memcpy(fkey, key, len); --fkey[len-1]; flen = len; } /* check hattrie_find_leq functionality */ dkey = realloc(dkey, len); memcpy(dkey, key, len); ++dkey[len-1]; value_t *fp = NULL; int r = hattrie_find_leq(T, dkey, len, &fp); if (*fp != *u || r != -1) { fprintf(stderr, "[error] hattrie_find_leq should find %lu, " "but found prev=%lu, rval=%d\n", *u, *fp, r); } hattrie_iter_next(i); } hattrie_iter_free(i); /* check before first key */ value_t *fp = NULL; int r = hattrie_find_leq(T, fkey, flen, &fp); if (r != 1 || fp != NULL) { fprintf(stderr, "[error] hattrie_find_leq should return 1 and NULL for " "string < first string, returned %d (%p)\n", r, (void*)fp); } free(fkey); free(dkey); fprintf(stderr, "done.\n"); }
void hattrie_iter_next(hattrie_iter_t* i) { do { if (hattrie_iter_finished(i)) return; if (i->i != NULL && !ahtable_iter_finished(i->i)) { ahtable_iter_next(i->i); } else if (i->has_nil_key) { i->has_nil_key = false; i->nil_val = 0; hattrie_iter_nextnode(i); } hattrie_iter_step(i); } while (i->prefix_len && hattrie_iter_prefix_not_match(i)); }
void test_hattrie_iteration() { fprintf(stderr, "iterating through %zu keys ... \n", k); hattrie_iter_t* i = hattrie_iter_begin(T, false); size_t count = 0; value_t* u; value_t v; size_t len; const char* key; while (!hattrie_iter_finished(i)) { ++count; key = hattrie_iter_key(i, &len); u = hattrie_iter_val(i); v = str_map_get(M, key, len); if (*u != v) { if (v == 0) { fprintf(stderr, "[error] incorrect iteration (%lu, %lu)\n", *u, v); } else { fprintf(stderr, "[error] incorrect iteration tally (%lu, %lu)\n", *u, v); } } // this way we will see an error if the same key is iterated through // twice str_map_set(M, key, len, 0); hattrie_iter_next(i); } if (count != M->m) { fprintf(stderr, "[error] iterated through %zu element, expected %zu\n", count, M->m); } hattrie_iter_free(i); fprintf(stderr, "done.\n"); }
static bool hattrie_iter_prefix_not_match(hattrie_iter_t* i) { if (hattrie_iter_finished(i)) { return false; // can not advance the iter } if (i->level >= i->prefix_len) { return memcmp(i->key, i->prefix, i->prefix_len); } else if (i->has_nil_key) { return true; // subkey too short } size_t sublen; const char* subkey; subkey = ahtable_iter_key(i->i, &sublen); if (i->level + sublen < i->prefix_len) { return true; // subkey too short } return memcmp(i->key, i->prefix, i->level) || memcmp(subkey, i->prefix + i->level, (i->prefix_len - i->level)); }
hattrie_t* hattrie_dup(const hattrie_t* T, value_t (*nval)(value_t)) { hattrie_t *N = hattrie_create_n(T->bsize, &T->mm); /* assignment */ if (!nval) nval = hattrie_setval; /*! \todo could be probably implemented faster */ size_t l = 0; const char *k = 0; hattrie_iter_t *i = hattrie_iter_begin(T, false); while (!hattrie_iter_finished(i)) { k = hattrie_iter_key(i, &l); *hattrie_get(N, k, l) = nval(*hattrie_iter_val(i)); hattrie_iter_next(i); } hattrie_iter_free(i); return N; }
const char* hattrie_iter_key(hattrie_iter_t* i, size_t* len) { if (hattrie_iter_finished(i)) return NULL; size_t sublen; const char* subkey; if (i->has_nil_key) { subkey = NULL; sublen = 0; } else subkey = ahtable_iter_key(i->i, &sublen); if (i->keysize < i->level + sublen + 1) { while (i->keysize < i->level + sublen + 1) i->keysize *= 2; i->key = realloc_or_die(i->key, i->keysize * sizeof(char)); } memcpy(i->key + i->level, subkey, sublen); i->key[i->level + sublen] = '\0'; if (len) *len = i->level + sublen; return i->key; }
void test_hattrie_sorted_iteration() { fprintf(stderr, "iterating in order through %zu keys ... \n", k); hattrie_iter_t* i = hattrie_iter_begin(T, true); size_t count = 0; value_t* u; value_t v; char* key_copy = malloc(m_high + 1); char* prev_key = malloc(m_high + 1); memset(prev_key, 0, m_high + 1); size_t prev_len = 0; const char *key = NULL; size_t len = 0; while (!hattrie_iter_finished(i)) { memcpy(prev_key, key_copy, len); prev_key[len] = '\0'; prev_len = len; ++count; key = hattrie_iter_key(i, &len); /* memory for key may be changed on iter, copy it */ strncpy(key_copy, key, len); if (prev_key != NULL && cmpkey(prev_key, prev_len, key, len) > 0) { fprintf(stderr, "[error] iteration is not correctly ordered.\n"); } u = hattrie_iter_val(i); v = str_map_get(M, key, len); if (*u != v) { if (v == 0) { fprintf(stderr, "[error] incorrect iteration (%lu, %lu)\n", *u, v); } else { fprintf(stderr, "[error] incorrect iteration tally (%lu, %lu)\n", *u, v); } } // this way we will see an error if the same key is iterated through // twice str_map_set(M, key, len, 0); hattrie_iter_next(i); } if (count != M->m) { fprintf(stderr, "[error] iterated through %zu element, expected %zu\n", count, M->m); } hattrie_iter_free(i); free(prev_key); free(key_copy); fprintf(stderr, "done.\n"); }
int main(int argc, char* argv[]) { if (argc < 2) { fprintf(stderr, "Usage: bam-summarize reads.bam\n"); exit(EXIT_FAILURE); } samfile_t* f = samopen(argv[1], "rb", NULL); if (f == NULL) { fprintf(stderr, "can't open bam file %s\n", argv[1]); exit(1); } bam1_t* b = bam_init1(); hattrie_t* T = hattrie_create(); char* qname = NULL; size_t qname_size = 0; size_t j, n = 0; uint32_t* cigar; uint32_t cigar_op, cigar_len; read_stat_t** val; while (samread(f, b) >= 0) { if (++n % 1000000 == 0) { fprintf(stderr, "\t%zu alignments\n", n); } bool perfect = true; bool spliced = false; bool gapped = false; cigar = bam1_cigar(b); for (j = 0; j < b->core.n_cigar; ++j) { cigar_op = cigar[j] & BAM_CIGAR_MASK; cigar_len = cigar[j] >> BAM_CIGAR_SHIFT; if (cigar_op == BAM_CREF_SKIP) { if (cigar_len < min_splice_length) gapped = true; else spliced = true; } else if (cigar_op != BAM_CMATCH) perfect = false; if (cigar_op == BAM_CSOFT_CLIP || cigar_op == BAM_CHARD_CLIP) break; } /* Skip any clipped alignments. We don't want your kind! */ if (cigar_op == BAM_CSOFT_CLIP || cigar_op == BAM_CHARD_CLIP) continue; /* Hack the read to include mate information. */ if (b->core.flag & BAM_FPAIRED) { if (qname_size < b->core.l_qname + 3) { qname_size = b->core.l_qname + 3; qname = realloc(qname, qname_size); } memcpy(qname, bam1_qname(b), b->core.l_qname); if (b->core.flag & BAM_FREAD1) { qname[b->core.l_qname] = '/'; qname[b->core.l_qname + 1] = '2'; qname[b->core.l_qname + 2] = '\0'; } else { qname[b->core.l_qname] = '/'; qname[b->core.l_qname + 1] = '1'; qname[b->core.l_qname + 2] = '\0'; } val = (read_stat_t**) hattrie_get(T, qname, b->core.l_qname + 2); } else { val = (read_stat_t**) hattrie_get(T, bam1_qname(b), b->core.l_qname); } if (*val == NULL) { *val = malloc(sizeof(read_stat_t)); memset(*val, 0, sizeof(read_stat_t)); } (*val)->aln_count++; if (perfect) { if (spliced) (*val)->spliced_perfect_cnt++; else (*val)->unspliced_perfect_cnt++; } if (spliced) (*val)->spliced_cnt++; if (gapped) (*val)->gapped_cnt++; } printf("alignment_count\t%zu\n", n); printf("read_count\t%zu\n", hattrie_size(T)); /* print stats from the table */ uint32_t multi_count = 0; uint32_t unspliced_perfect_cnt = 0; uint32_t spliced_perfect_cnt = 0; uint32_t spliced_cnt = 0; uint32_t gapped_cnt = 0; /* excluding multireads */ uint32_t unique_unspliced_perfect_cnt = 0; uint32_t unique_spliced_perfect_cnt = 0; uint32_t unique_spliced_cnt = 0; uint32_t unique_gapped_cnt = 0; hattrie_iter_t* i; for (i = hattrie_iter_begin(T); !hattrie_iter_finished(i); hattrie_iter_next(i)) { val = (read_stat_t**) hattrie_iter_val(i); if ((*val)->aln_count == 1) { unique_unspliced_perfect_cnt += (*val)->unspliced_perfect_cnt; unique_spliced_perfect_cnt += (*val)->spliced_perfect_cnt; unique_spliced_cnt += (*val)->spliced_cnt; unique_gapped_cnt += (*val)->gapped_cnt; } else multi_count++; unspliced_perfect_cnt += (*val)->unspliced_perfect_cnt; spliced_perfect_cnt += (*val)->spliced_perfect_cnt; spliced_cnt += (*val)->spliced_cnt; gapped_cnt += (*val)->gapped_cnt; } hattrie_iter_free(i); printf("multi_count\t%u\n", multi_count); printf("unspliced_perfect_cnt\t%u\n", unspliced_perfect_cnt); printf("spliced_perfect_cnt\t%u\n", spliced_perfect_cnt); printf("spliced_cnt\t%u\n", spliced_cnt); printf("gapped_cnt\t%u\n", gapped_cnt); printf("unique_unspliced_perfect_cnt\t%u\n", unique_unspliced_perfect_cnt); printf("unique_spliced_perfect_cnt\t%u\n", unique_spliced_perfect_cnt); printf("unique_spliced_cnt\t%u\n", unique_spliced_cnt); printf("unique_gapped_cnt\t%u\n", unique_gapped_cnt); /* free the table */ for (i = hattrie_iter_begin(T); !hattrie_iter_finished(i); hattrie_iter_next(i)) { free(* (read_stat_t**) hattrie_iter_val(i)); } hattrie_iter_free(i); hattrie_free(T); free(qname); bam_destroy1(b); return 0; }
int main(int argc, char *argv[]) { plan_lazy(); /* Random keys. */ srand(time(NULL)); unsigned key_count = 100000; char **keys = malloc(sizeof(char*) * key_count); for (unsigned i = 0; i < key_count; ++i) { keys[i] = str_key_rand(KEY_MAXLEN); } /* Sort random keys. */ str_key_sort(keys, key_count); /* Create trie */ value_t *val = NULL; hattrie_t *trie = hattrie_create(); ok(trie != NULL, "hattrie: create"); /* Insert keys */ bool passed = true; size_t inserted = 0; for (unsigned i = 0; i < key_count; ++i) { val = hattrie_get(trie, keys[i], strlen(keys[i]) + 1); if (!val) { passed = false; break; } if (*val == NULL) { *val = keys[i]; ++inserted; } } ok(passed, "hattrie: insert"); /* Check total insertions against trie weight. */ is_int(hattrie_weight(trie), inserted, "hattrie: trie weight matches insertions"); /* Build order-index. */ hattrie_build_index(trie); /* Lookup all keys */ passed = true; for (unsigned i = 0; i < key_count; ++i) { val = hattrie_tryget(trie, keys[i], strlen(keys[i]) + 1); if (val && (*val == keys[i] || strcmp(*val, keys[i]) == 0)) { continue; } else { diag("hattrie: mismatch on element '%u'", i); passed = false; break; } } ok(passed, "hattrie: lookup all keys"); /* Lesser or equal lookup. */ passed = true; for (unsigned i = 0; i < key_count; ++i) { if (!str_key_find_leq(trie, keys, i, key_count)) { passed = false; for (int off = -10; off < 10; ++off) { int k = (int)i + off; if (k < 0 || k >= key_count) { continue; } diag("[%u/%d]: %s%s", i, off, off == 0?">":"",keys[k]); } break; } } ok(passed, "hattrie: find lesser or equal for all keys"); /* Next lookup. */ passed = true; for (unsigned i = 0; i < key_count - 1 && passed; ++i) { value_t *val; hattrie_find_next(trie, keys[i], strlen(keys[i]), &val); passed = val && *val == (void *)keys[(i + 1)]; } ok(passed, "hattrie: find next for all keys"); /* Unsorted iteration */ size_t iterated = 0; hattrie_iter_t *it = hattrie_iter_begin(trie, false); while (!hattrie_iter_finished(it)) { ++iterated; hattrie_iter_next(it); } is_int(inserted, iterated, "hattrie: unsorted iteration"); hattrie_iter_free(it); /* Sorted iteration. */ char key_buf[KEY_MAXLEN] = {'\0'}; iterated = 0; it = hattrie_iter_begin(trie, true); while (!hattrie_iter_finished(it)) { size_t cur_key_len = 0; const char *cur_key = hattrie_iter_key(it, &cur_key_len); if (iterated > 0) { /* Only if previous exists. */ if (strcmp(key_buf, cur_key) > 0) { diag("'%s' <= '%s' FAIL\n", key_buf, cur_key); break; } } ++iterated; memcpy(key_buf, cur_key, cur_key_len); hattrie_iter_next(it); } is_int(inserted, iterated, "hattrie: sorted iteration"); hattrie_iter_free(it); /* Cleanup */ for (unsigned i = 0; i < key_count; ++i) { free(keys[i]); } free(keys); hattrie_free(trie); return 0; }
int proc_update_privileges(int uid, int gid) { #ifdef HAVE_SETGROUPS /* Drop supplementary groups. */ if ((uid_t)uid != getuid() || (gid_t)gid != getgid()) { if (setgroups(0, NULL) < 0) { log_server_warning("Failed to drop supplementary groups" " for uid '%d' (%s).\n", getuid(), strerror(errno)); } # ifdef HAVE_INITGROUPS struct passwd *pw; if ((pw = getpwuid(uid)) == NULL) { log_server_warning("Failed to get passwd entry" " for uid '%d' (%s).\n", uid, strerror(errno)); } else { if (initgroups(pw->pw_name, gid) < 0) { log_server_warning("Failed to set supplementary groups" " for uid '%d' (%s).\n", uid, strerror(errno)); } } # endif /* HAVE_INITGROUPS */ } #endif /* HAVE_SETGROUPS */ /* Watch uid/gid. */ if ((gid_t)gid != getgid()) { log_server_info("Changing group id to '%d'.\n", gid); if (setregid(gid, gid) < 0) { log_server_error("Failed to change gid to '%d'.\n", gid); } } if ((uid_t)uid != getuid()) { log_server_info("Changing user id to '%d'.\n", uid); if (setreuid(uid, uid) < 0) { log_server_error("Failed to change uid to '%d'.\n", uid); } } /* Check storage writeability. */ int ret = KNOT_EOK; const bool sorted = false; hattrie_iter_t *z_iter = hattrie_iter_begin(conf()->zones, sorted); if (z_iter == NULL) { return KNOT_ERROR; } for (; !hattrie_iter_finished(z_iter); hattrie_iter_next(z_iter)) { conf_zone_t *zone = (conf_zone_t *)*hattrie_iter_val(z_iter); char *lfile = strcdup(zone->storage, "/knot.lock"); assert(lfile != NULL); FILE* fp = fopen(lfile, "w"); if (fp == NULL) { log_server_warning("Storage directory '%s' is not " "writeable.\n", zone->storage); ret = KNOT_EACCES; } else { fclose(fp); unlink(lfile); } free(lfile); if (ret != KNOT_EOK) { break; } } hattrie_iter_free(z_iter); return ret; }