static int
mkfstab(void)
{
char *cmd = "/usr/lib/partconf/mkfstab";
append_message("partconf: Create fstab\n");
return system(cmd);
}
void new_list(t_app *app, int *listing, char *found)
{
char *found1;
*found = 0;
*app->screen->users_text = 0;
if ((found1 = strchr(found + 1, 31)))
{
*found1 = 0;
append_message(&(app->screen->users_text), found + 1);
strcpy(found, found1 + 1);
}
else
{
*listing = 1;
append_message(&(app->screen->users_text), found + 1);
}
}
static ::testing::AssertionResult UriIsExpected(const char *expected_var,
const char *actual_var,
const uri_expected &expected,
const htp_uri_t *actual) {
std::stringstream msg;
bool equal=true;
if (! bstr_equal_c(actual->scheme, expected.scheme)) {
equal = false;
append_message(msg, "scheme", expected.scheme, actual->scheme);
}
if (! bstr_equal_c(actual->username, expected.username)) {
equal = false;
append_message(msg, "username", expected.username, actual->username);
}
if (! bstr_equal_c(actual->password, expected.password)) {
equal = false;
append_message(msg, "password", expected.password, actual->password);
}
if (! bstr_equal_c(actual->hostname, expected.hostname)) {
equal = false;
append_message(msg, "hostname", expected.hostname, actual->hostname);
}
if (! bstr_equal_c(actual->port, expected.port)) {
equal = false;
append_message(msg, "port", expected.port, actual->port);
}
if (! bstr_equal_c(actual->path, expected.path)) {
equal = false;
append_message(msg, "path", expected.path, actual->path);
}
if (! bstr_equal_c(actual->query, expected.query)) {
equal = false;
append_message(msg, "query", expected.query, actual->query);
}
if (! bstr_equal_c(actual->fragment, expected.fragment)) {
equal = false;
append_message(msg, "fragment", expected.fragment, actual->fragment);
}
if (equal) {
return ::testing::AssertionSuccess();
} else {
return ::testing::AssertionFailure() << msg.str();
}
}
void hwu_assert_put_message(const char* exp, const char* file, const int line, const char* format, ...)
{
char out[1024] = {0};
char line_string[32] = {0};
char user_message[256] = {0};
va_list user_args;
strcat(out, ASSERT_LINE_BEGIN);
strcat(out, ASSERT_MESSAGE);
append_message(out, "exp :", exp);
append_message(out, "file :", file);
append_message(out, "line :", itoa(line, line_string, 8));
va_start(user_args, format);
vsprintf(user_message, format, user_args);
va_end(user_args);
append_message(out, "user :", user_message);
strcat(out, ASSERT_LINE_END);
hwu_debug_print(out);
}
int check_before_append(t_app *app, char *buffer)
{
static int listing;
char *found;
if (!listing && (found = strchr(buffer, 31)))
{
new_list(app, &listing, found);
return (1);
}
if (listing && (found = strchr(buffer, 31)))
{
*found = 0;
append_message(&(app->screen->users_text), buffer);
strcpy(buffer, found + 1);
listing = 0;
return (1);
}
if (listing)
append_message(&(app->screen->users_text), buffer);
return (0);
}
/*
* add each top level reply in the thread, and then add each
* reply to the top level replies
*/
static void append_thread(CONTEXT *ctx, notmuch_thread_t *thread)
{
notmuch_messages_t *msgs;
for (msgs = notmuch_thread_get_toplevel_messages(thread);
notmuch_messages_valid(msgs);
notmuch_messages_move_to_next(msgs)) {
notmuch_message_t *m = notmuch_messages_get(msgs);
append_message(ctx, m);
append_replies(ctx, m);
notmuch_message_destroy(m);
}
}
/*
* add all the replies to a given messages into the display.
* Careful, this calls itself recursively to make sure we get
* everything.
*/
static void append_replies(CONTEXT *ctx, notmuch_message_t *top)
{
notmuch_messages_t *msgs;
for (msgs = notmuch_message_get_replies(top);
notmuch_messages_valid(msgs);
notmuch_messages_move_to_next(msgs)) {
notmuch_message_t *m = notmuch_messages_get(msgs);
append_message(ctx, m);
/* recurse through all the replies to this message too */
append_replies(ctx, m);
notmuch_message_destroy(m);
}
}
static void read_mesgs_query(CONTEXT *ctx, notmuch_query_t *q, int dedup)
{
struct nm_ctxdata *data = get_ctxdata(ctx);
int limit;
notmuch_messages_t *msgs;
if (!data)
return;
limit = get_limit(data);
for (msgs = notmuch_query_search_messages(q);
notmuch_messages_valid(msgs) &&
(limit == 0 || ctx->msgcount < limit);
notmuch_messages_move_to_next(msgs)) {
notmuch_message_t *m = notmuch_messages_get(msgs);
append_message(ctx, q, m, dedup);
notmuch_message_destroy(m);
}
}
void nmea_sentence_received(const char *sentence,
unsigned int length,
unsigned char sentences,
unsigned char sentencenum) {
append_message(sentence);
if (sentences == 1) {
if (send_nmea( sentence, length) == -1) abort();
if (debug_nmea) fprintf(stderr, "%s", sentence);
} else {
if (buffer_count + length < MAX_BUFFER_LENGTH) {
memcpy(&buffer[buffer_count], sentence, length);
buffer_count += length;
} else {
buffer_count=0;
}
if (sentences == sentencenum && buffer_count > 0) {
if (send_nmea( buffer, buffer_count) == -1) abort();
if (debug_nmea) fprintf(stderr, "%s", buffer);
buffer_count=0;
};
}
}
static void
finish(void)
{
int i, ret;
char *cmd, *mntpt, *errq = NULL, *fs;
// Sort the partitions according to the order they have to be mounted
qsort(parts, part_count, sizeof(struct partition *), mountpoint_sort_func);
for (i = 0; i < part_count; i++) {
fs = parts[i]->op.filesystem;
if (fs == NULL)
fs = parts[i]->fstype;
else {
// Create the file system/swap
if (strcmp(fs, "swap") == 0) {
append_message("partconf: Creating swap on %s\n", parts[i]->path);
asprintf(&cmd, "mkswap %s >/dev/null 2>>/var/log/messages", parts[i]->path);
ret = system(cmd);
free(cmd);
if (ret != 0) {
errq = "partconf/failed-mkswap";
break;
}
} else {
char *mkfs_opts="";
/* mkfs.reiserfs is interactive unless passed a -q */
if (strcmp(fs, "reiserfs") == 0) {
mkfs_opts="-q";
}
/* mkfs.xfs will not overwrite existing filesystems unless
* one passes -f. at this point, user has claimed "yes, do
* as I say!" so let's force it here. */
else if (strcmp(fs, "xfs") == 0) {
mkfs_opts="-f";
}
append_message("partconf: Creating %s file system on %s\n", fs, parts[i]->path);
asprintf(&cmd, "mkfs.%s %s %s >/dev/null 2>>/var/log/messages", fs, mkfs_opts, parts[i]->path);
ret = system(cmd);
free(cmd);
if (ret != 0) {
errq = "partconf/failed-mkfs";
debconf_subst(debconf,errq, "FS", parts[i]->op.filesystem);
break;
}
}
}
if (fs != NULL) {
if (strcmp(fs, "swap") == 0 && !check_proc_swaps(parts[i]->path)) {
// Activate swap
append_message("partconf: Activating swap on %s\n", parts[i]->path);
asprintf(&cmd, "swapon %s >/dev/null 2>>/var/log/messages", parts[i]->path);
ret = system(cmd);
free(cmd);
/*
* Since we check if the swap is already activated, it may
* make sense to make this fatal. For now, it is, anyway.
*/
if (ret != 0) {
errq = "partconf/failed-swapon";
break;
}
} else if (parts[i]->op.mountpoint != NULL) {
// And mount
append_message("partconf: Mounting %s on %s\n",
parts[i]->path, parts[i]->op.mountpoint);
asprintf(&mntpt, "/target%s", parts[i]->op.mountpoint);
makedirs(mntpt);
fs = parts[i]->op.filesystem ? parts[i]->op.filesystem : parts[i]->fstype;
ret = mount(parts[i]->path, mntpt, fs, 0xC0ED0000, NULL);
// Ignore failure due to unknown filesystem
if (ret < 0 && errno != ENODEV) {
append_message("mount: %s\n", strerror(errno));
errq = "partconf/failed-mount";
debconf_subst(debconf, errq, "MOUNT", mntpt);
free(mntpt);
break;
}
free(mntpt);
}
}
}
if (errq != NULL) {
debconf_subst(debconf, errq, "PARTITION", parts[i]->path);
debconf_input(debconf,"critical", errq);
debconf_go(debconf);
exit(30);
}
mkfstab();
exit(0);
}
FILE* io_handler(FILE* file, int file_num,struct parameters* param)
{
char command[1000];
char tmp[1000];
//int i = 0;
int gzcat = -1;
if(access("/usr/bin/gzcat", X_OK) == 0){
gzcat = 1;
}else if(access("/bin/gzcat", X_OK) == 0){
gzcat = 1;
}else if(access("/usr/bin/zcat", X_OK) == 0){
gzcat = 0;
}else if(access("/bin/zcat", X_OK) == 0){
gzcat = 0;
}
param->gzipped = 0;
param->bzipped = 0;
param->sam = 0;
param->fasta = 0;
if(!file_exists(param->infile[file_num])){
sprintf(param->buffer,"ERROR: Cannot find input file: %s\n",param->infile[file_num] );
param->messages = append_message(param->messages, param->buffer);
free_param(param);
exit(EXIT_FAILURE);
}
if(!strcmp(".sam", param->infile[file_num] + (strlen(param->infile[file_num] ) - 4))){
param->sam = 1;
}else if (!strcmp(".bam", param->infile[file_num] + (strlen(param->infile[file_num] ) - 4))){
param->sam = 2;
}else if (!strcmp(".fa", param->infile[file_num] + (strlen(param->infile[file_num] ) - 3))){
param->sam = 0;
param->fasta = 1;
}else if (!strcmp(".fq", param->infile[file_num] + (strlen(param->infile[file_num] ) - 3))){
param->sam = 0;
}else if (!strcmp(".fastq", param->infile[file_num] + (strlen(param->infile[file_num] ) - 6))){
param->sam = 0;
}else if (!strcmp(".fastaq", param->infile[file_num] + (strlen(param->infile[file_num] ) - 7))){
param->sam = 0;
}else if (!strcmp(".fasta", param->infile[file_num] + (strlen(param->infile[file_num] ) - 6))){
param->sam = 0;
param->fasta = 1;
}else if(!strcmp(".sam.gz", param->infile[file_num] + (strlen(param->infile[file_num] ) - 7))){
param->sam = 1;
param->gzipped = 1;
}else if (!strcmp(".bam.gz", param->infile[file_num] + (strlen(param->infile[file_num] ) - 7))){
param->sam = 2;
param->gzipped = 1;
}else if (!strcmp(".fa.gz", param->infile[file_num] + (strlen(param->infile[file_num] ) - 6))){
param->sam = 0;
param->fasta = 1;
param->gzipped = 1;
}else if (!strcmp(".fq.gz", param->infile[file_num] + (strlen(param->infile[file_num] ) - 6))){
param->sam = 0;
param->gzipped = 1;
}else if (!strcmp(".fastq.gz", param->infile[file_num] + (strlen(param->infile[file_num] ) - 9))){
param->sam = 0;
param->gzipped = 1;
}else if (!strcmp(".fastaq.gz", param->infile[file_num] + (strlen(param->infile[file_num] ) - 10))){
param->sam = 0;
param->gzipped = 1;
}else if (!strcmp(".fasta.gz", param->infile[file_num] + (strlen(param->infile[file_num] ) - 9))){
param->sam = 0;
param->gzipped = 1;
}else if (!strcmp(".fastq.bz2", param->infile[file_num] + (strlen(param->infile[file_num] ) - 10))){
param->sam = 0;
param->bzipped = 1;
}else if (!strcmp(".fq.bz2", param->infile[file_num] + (strlen(param->infile[file_num] ) - 7))){
param->sam = 0;
param->bzipped = 1;
}else{
sprintf(param->buffer,"ERROR: Cannot recognize format for file: %s\n", param->infile[file_num]);
param->messages = append_message(param->messages, param->buffer);
free_param(param);
exit(EXIT_FAILURE);
param->sam = -1;
}
if(param->gzipped && gzcat == -1){
sprintf(param->buffer,"ERROR: Cannot find gzcat / zcat on your system. Try gzcat <infile> | samstat -f sam/bam/fa/fq\n");
param->messages = append_message(param->messages, param->buffer);
free_param(param);
exit(EXIT_FAILURE);
}
if(file_num == -1){
if(param->sam == 2){
command[0] = 0;
if(!param->filter){
strcat ( command, "samtools view -F 768 ");
}else{
strcat ( command, "samtools view -F ");
sprintf (tmp, "%s ",param->filter);
strcat ( command, tmp);
}
sprintf (tmp, "%s ","-");
strcat ( command, tmp);
if (!(file = popen(command, "r"))) {
sprintf(param->buffer,"ERROR: Cannot open bam file '%s' with command:%s\n",param->infile[file_num],command);
param->messages = append_message(param->messages, param->buffer);
free_param(param);
exit(EXIT_FAILURE);
}
}else if(param->sam == 1){
command[0] = 0;
if(!param->filter){
strcat ( command, "samtools view -SF 768 ");
}else{
strcat ( command, "samtools view -SF ");
sprintf (tmp, "%s ",param->filter);
strcat ( command, tmp);
}
sprintf (tmp, "%s ", "-");
strcat ( command, tmp);
if (!(file = popen(command, "r"))) {
sprintf(param->buffer,"ERROR: Cannot open bam file '%s' with command:%s\n",param->infile[file_num],command);
param->messages = append_message(param->messages, param->buffer);
free_param(param);
exit(EXIT_FAILURE);
}
}else{
file = stdin;
}
}else{
if(param->sam == 2){
command[0] = 0;
if(param->bzipped){
strcat ( command, "bzcat ");
if(!param->filter){
sprintf (tmp, "%s | samtools view -F 768 - ", param->infile[file_num]);
strcat ( command, tmp);
}else{
sprintf (tmp, "%s | samtools view -F ", param->infile[file_num]);
strcat ( command, tmp);
sprintf (tmp, "%s - ",param->filter);
strcat ( command, tmp);
}
}else if(param->gzipped){
if(gzcat == 1){
strcat ( command, "gzcat ");
}else{
strcat ( command, "zcat ");
}
if(!param->filter){
sprintf (tmp, "%s | samtools view -F 768 - ", param->infile[file_num]);
strcat ( command, tmp);
}else{
sprintf (tmp, "%s | samtools view -F ", param->infile[file_num]);
strcat ( command, tmp);
sprintf (tmp, "%s - ",param->filter);
strcat ( command, tmp);
}
}else{
if(!param->filter){
strcat ( command, "samtools view -F 768 ");
}else{
strcat ( command, "samtools view -F ");
sprintf (tmp, "%s ",param->filter);
strcat ( command, tmp);
}
sprintf (tmp, "%s ", param->infile[file_num]);
strcat ( command, tmp);
}
if (!(file = popen(command, "r"))) {
sprintf(param->buffer,"Cannot open bam file '%s' with command:%s\n",param->infile[file_num],command);
param->messages = append_message(param->messages, param->buffer);
free_param(param);
exit(EXIT_FAILURE);
}
}else if(param->sam == 1){
command[0] = 0;
if(param->gzipped){
if(gzcat == 1){
strcat ( command, "gzcat ");
}else{
strcat ( command, "zcat ");
}
if(!param->filter){
sprintf (tmp, "%s | samtools view -SF 768 - ", param->infile[file_num]);
strcat ( command, tmp);
}else{
sprintf (tmp, "%s | samtools view -SF ", param->infile[file_num]);
strcat ( command, tmp);
sprintf (tmp, "%s - ",param->filter);
strcat ( command, tmp);
}
}else{
if(!param->filter){
strcat ( command, "samtools view -SF 768 ");
}else{
strcat ( command, "samtools view -SF ");
sprintf (tmp, "%s ",param->filter);
strcat ( command, tmp);
}
sprintf (tmp, "%s ", param->infile[file_num]);
strcat ( command, tmp);
}
if (!(file = popen(command, "r"))) {
sprintf(param->buffer,"Cannot open bam file '%s' with command:%s\n",param->infile[file_num],command);
param->messages = append_message(param->messages, param->buffer);
free_param(param);
exit(EXIT_FAILURE);
}
}else{
command[0] = 0;
if(param->bzipped){
strcat ( command, "bzcat ");
}else if(param->gzipped){
if(gzcat == 1){
strcat ( command, "gzcat ");
}else{
strcat ( command, "zcat ");
}
}else{
strcat ( command, "cat ");
}
sprintf (tmp, "%s ", param->infile[file_num]);
strcat ( command, tmp);
//fprintf(stderr,"%s\n",command);
if (!(file = popen(command, "r"))) {
sprintf(param->buffer,"Cannot open bam file '%s' with command:%s\n",param->infile[file_num],command);
param->messages = append_message(param->messages, param->buffer);
free_param(param);
exit(EXIT_FAILURE);
}
}
}
return file;
}
int read_fasta_fastq(struct read_info** ri,struct parameters* param,FILE *file)
{
int park_pos = -1;
char line[MAX_LINE];
int i;//,j;
int seq_p = 0;
int set = 0;
int len = 0;
int size = 0;
ri = clear_read_info(ri, param->num_query);
while(fgets(line, MAX_LINE, file)){
if((line[0] == '@' && !set)|| (line[0] == '>' && !set)){
//set sequence length of previous read
//check if there is still space....
//if(param->num_query == size){
// fseek (file , - strlen(line) , SEEK_CUR);
// return size;
//}
park_pos++;
len = 0;
seq_p = 1;
for(i = 1;i < MAX_LINE;i++){
len++;
if(iscntrl((int)line[i])){
break;
}
}
//ri[park_pos]->hits[0] = 0;
//ri[park_pos]->strand[0] = 0;
MMALLOC(ri[park_pos]->name,sizeof(unsigned char)* (len+1));
for(i = 1;i < MAX_LINE;i++){
if(iscntrl((int)line[i])){
ri[park_pos]->name[i-1] = 0;
break;
}
if(isspace((int)line[i])){
ri[park_pos]->name[i-1] = ';';
}
ri[park_pos]->name[i-1] = line[i];
}
//fprintf(stderr,"LEN:%d %s\n",len,ri[park_pos]->name);
set = 1;
size++;
//get ready to read quality if present
}else if(line[0] == '+' && !set){
seq_p = 0;
set = 1;
//reading sequence or quality
}else{
if(set){
if(seq_p){
len = 0;
for(i = 0;i < MAX_LINE;i++){
len++;
if(iscntrl((int)line[i])){
break;
}
}
//fprintf(stderr,"SEQ LEN:%d %s\n",len,line);
MMALLOC(ri[park_pos]->seq,sizeof(unsigned char)* (len+1));
MMALLOC(ri[park_pos]->labels, sizeof(unsigned char)* (len+1));
for(i = 0;i < MAX_LINE;i++){
if(iscntrl((int)line[i])){
ri[park_pos]->seq[i] = 0;
ri[park_pos]->labels[i] = 0;
break;
}
ri[park_pos]->seq[i] = nuc_code[(int)line[i]];
ri[park_pos]->labels[i] = 0;
}
ri[park_pos]->len = len-1;
}else{
len = 0;
for(i = 0;i < MAX_LINE;i++){
len++;
if(iscntrl((int)line[i])){
break;
}
}
if(len-1 != ri[park_pos]->len ){
sprintf(param->buffer,"ERROR: Length of sequence and base qualities differ!.\n");
param->messages = append_message(param->messages, param->buffer);
free_param(param);
exit(EXIT_FAILURE);
}
//fprintf(stderr,"QUAL LEN:%d\n",len);
MMALLOC(ri[park_pos]->qual,sizeof(unsigned char)* (len+1));
for(i = 0;i < MAX_LINE;i++){
if(iscntrl((int)line[i])){
ri[park_pos]->qual[i] = 0;
break;
}
ri[park_pos]->qual[i] = line[i];
}
}
}
set = 0;
}
if(param->num_query == size ){//here I know I am in the last entry AND filled the quality...
if(!param->fasta && ri[park_pos]->qual){
return size;
}
if(param->fasta && ri[park_pos]->seq){
return size;
}
}
}
return size;
}
