void
test_err_handler
(void)
{
int obs[] = {6,2,2,3,2,0,1,2,5,2,0,0,0};
zinb_par_t *par = NULL;
set_zinb_err_handler(dummy_handler);
redirect_stderr();
set_alloc_failure_countdown_to(0);
par = mle_zinb(obs, 13);
reset_alloc();
unredirect_stderr();
test_assert(par == NULL);
test_assert(strcmp(caught_in_stderr(), "dummy") == 0);
redirect_stderr();
set_alloc_failure_countdown_to(0);
par = mle_zinb(obs, 13);
reset_alloc();
unredirect_stderr();
test_assert(par == NULL);
test_assert(strcmp(caught_in_stderr(), "dummy") == 0);
// Reset error handler.
set_zinb_err_handler(NULL);
redirect_stderr();
set_alloc_failure_countdown_to(0);
par = mle_zinb(obs, 13);
reset_alloc();
unredirect_stderr();
test_assert(par == NULL);
test_assert(strncmp(caught_in_stderr(), "memory error", 12) == 0);
redirect_stderr();
set_alloc_failure_countdown_to(0);
par = mle_nb(obs, 13);
reset_alloc();
unredirect_stderr();
test_assert(par == NULL);
test_assert(strncmp(caught_in_stderr(), "memory error", 12) == 0);
free(par);
}
void
test_compress_histo
(void)
{
histo_t *histo = new_histo();
test_assert_critical(histo != NULL);
for (size_t i = 0 ; i < 4096 ; i += 2) {
test_assert(histo_push(&histo, i) == 0);
}
tab_t *tab;
tab = compress_histo(histo);
test_assert_critical(tab != NULL);
test_assert(tab->size == 2048);
for (size_t i = 0 ; i < tab->size ; i++) {
test_assert(tab->val[i] == 2*i);
test_assert(tab->num[i] == 1);
}
free(tab);
redirect_stderr();
set_alloc_failure_rate_to(1.0);
tab = compress_histo(histo);
reset_alloc();
unredirect_stderr();
test_assert(tab == NULL);
test_assert(strcmp(caught_in_stderr(), "") != 0);
free(histo);
return;
}
void
test_io_stream_open
(void)
{
iostream_t * stream;
// Test invalid arguments.
redirect_stderr();
stream = io_stream_open("fake-file.txt");
test_assert(stream == NULL);
unredirect_stderr();
// Load files.
stream = io_stream_open("examples/io_input.raw");
test_assert(stream != NULL);
io_stream_free(stream);
stream = io_stream_open("examples/io_input.fasta");
test_assert(stream != NULL);
io_stream_free(stream);
stream = io_stream_open("examples/io_input.fastq");
test_assert(stream != NULL);
io_stream_free(stream);
}
void
test_mem_index_read
(void)
{
redirect_stderr();
index_t * index = index_build("examples/repeats.fa", "test_base30");
test_assert_critical(index != NULL);
test_assert(index_ann_new(25, 1, 1, index) == 0);
// Set alloc failure rate to 0.1.
set_alloc_failure_rate_to(0.1);
for (int i = 0; i < 1000; i++) {
index_t * index_i = index_read("test_base30");
index_free(index_i);
}
reset_alloc();
// Set alloc countdown 0->10.
for (int i = 0; i <= 200; i++) {
set_alloc_failure_countdown_to(i);
index_t * index_i = index_read("test_base30");
index_free(index_i);
}
reset_alloc();
index_free(index);
unredirect_stderr();
}
void
test_fail_mle_nb
(void)
{
int obs[] = {6,2,2,3,2,0,1,2,5,2};
zinb_par_t *par = NULL;
redirect_stderr();
set_alloc_failure_countdown_to(0);
par = mle_nb(obs, 10);
reset_alloc();
unredirect_stderr();
test_assert(par == NULL);
test_assert(strncmp(caught_in_stderr(), "memory error", 12) == 0);
redirect_stderr();
set_alloc_failure_countdown_to(1);
par = mle_nb(obs, 10);
reset_alloc();
unredirect_stderr();
test_assert(par == NULL);
test_assert(strncmp(caught_in_stderr(), "memory error", 12) == 0);
redirect_stderr();
set_alloc_failure_countdown_to(2);
par = mle_nb(obs, 10);
reset_alloc();
unredirect_stderr();
test_assert(par == NULL);
test_assert(strncmp(caught_in_stderr(), "memory error", 12) == 0);
redirect_stderr();
set_alloc_failure_countdown_to(3);
par = mle_nb(obs, 10);
reset_alloc();
unredirect_stderr();
test_assert_critical(par != NULL);
test_assert(strncmp(caught_in_stderr(), "$", 1) == 0);
free(par);
return;
}
void
test_mem_sar_get_range
(void)
{
sym_t * sym = sym_new_dna();
test_assert_critical(sym != NULL);
txt_t * txt = txt_new(sym);
test_assert_critical(txt != NULL);
test_assert(txt_append("TAGCNTCGACA", txt) == 0);
test_assert(txt_commit_seq("seq0",txt) == 0);
test_assert(txt_commit_rc(txt) == 0);
sar_t * sar = sar_build(txt);
test_assert_critical(sar != NULL);
int64_t * sa_buf = malloc(30*sizeof(int64_t));
test_assert_critical(sa_buf != NULL);
redirect_stderr();
// Set alloc failure rate to 0.1.
set_alloc_failure_rate_to(0.1);
for (int i = 0; i < 100; i++) {
sar_get_range(0,10,sa_buf,sar);
sar_get_range(10,5,sa_buf,sar);
sar_get_range(19,30,sa_buf,sar);
}
reset_alloc();
// Set alloc countdown 0->10.
for (int i = 0; i <= 10; i++) {
set_alloc_failure_countdown_to(i);
sar_get_range(0,10,sa_buf,sar);
sar_get_range(10,5,sa_buf,sar);
sar_get_range(19,30,sa_buf,sar);
}
reset_alloc();
free(sa_buf);
sar_free(sar);
txt_free(txt);
sym_free(sym);
unredirect_stderr();
}
void
test_mem_sar_file
(void)
{
sym_t * sym = sym_new_dna();
test_assert_critical(sym != NULL);
txt_t * txt = txt_new(sym);
test_assert_critical(txt != NULL);
test_assert(txt_append("TAGCNTCGACA", txt) == 0);
test_assert(txt_commit_seq("seq0",txt) == 0);
test_assert(txt_commit_rc(txt) == 0);
sar_t * sar = sar_build(txt);
test_assert_critical(sar != NULL);
sar_t * sar_i;
redirect_stderr();
// Set alloc failure rate to 0.1.
set_alloc_failure_rate_to(0.1);
for (int i = 0; i < 100; i++) {
sar_file_write("test30.sar", sar);
sar_i = sar_file_read("test30.sar");
sar_free(sar_i);
}
reset_alloc();
// Set alloc countdown 0->10.
for (int i = 0; i <= 10; i++) {
set_alloc_failure_countdown_to(i);
sar_file_write("test30.sar", sar);
sar_i = sar_file_read("test30.sar");
sar_free(sar_i);
}
reset_alloc();
sar_free(sar);
txt_free(txt);
sym_free(sym);
unredirect_stderr();
}
void
fail_non_critical
(
const char * assertion,
const char * file,
int lineno,
const char * function
)
// Handle failure of non critical assert statements.
// Set the test status to failed and update the display
// and print error message.
{
// If first failed assertion of the test
// case, update display for the user.
if (!TEST_CASE_FAILED) {
update_display_failed();
}
TEST_CASE_FAILED = 1;
// If stderr is redirected, we will need to
// take it back to display the error message.
int toggle_stderr = STDERR_OFF;
if (toggle_stderr) unredirect_stderr();
// Don't show more than 'MAX_N_ERROR_MSG', unless
// user passed the --showall or -a option.
if (N_ERROR_MSG++ < MAX_N_ERROR_MSG || SHOWALL) {
fprintf(stderr, "%s:%d: `%s'\n", file, lineno, assertion);
}
else if (N_ERROR_MSG == MAX_N_ERROR_MSG + 1) {
fprintf(stderr, "more than %d failed assertions...\n",
MAX_N_ERROR_MSG);
}
// Flush stderr and put it back as it was (ie redirect
// it if it was redirected, or leave it as is otherwise).
fflush(stderr);
if (toggle_stderr) redirect_stderr();
}
void
test_histo_push
(void)
{
histo_t *histo;
histo = new_histo();
test_assert_critical(histo != NULL);
for (size_t i = 0 ; i < (1 << 16) ; i++) {
test_assert(histo_push(&histo, i) == 0);
}
test_assert(histo->size == (1 << 16));
for (size_t i = 0 ; i < (1 << 16) ; i++) {
test_assert(histo->num[i] == 1);
}
free(histo);
histo = new_histo();
test_assert_critical(histo != NULL);
for (size_t i = (1 << 16) ; i > 0 ; i--) {
test_assert(histo_push(&histo, i-1) == 0);
}
test_assert(histo->size == 2*((1 << 16)-1));
for (size_t i = 0 ; i < (1 << 16) ; i++) {
test_assert(histo->num[i] == 1);
}
free(histo);
histo = new_histo();
test_assert_critical(histo != NULL);
redirect_stderr();
set_alloc_failure_rate_to(1.0);
test_assert(histo_push(&histo, HISTO_INIT_SIZE) == 1);
reset_alloc();
unredirect_stderr();
test_assert(strcmp(caught_in_stderr(), "") != 0);
free(histo);
return;
}
void
test_mem_index_build
(void)
{
redirect_stderr();
// Set alloc failure rate to 0.1.
set_alloc_failure_rate_to(0.1);
for (int i = 0; i < 1000; i++) {
index_t * index = index_build("examples/repeats.fa", "test_base20");
index_free(index);
}
reset_alloc();
// Set alloc countdown 0->10.
for (int i = 0; i <= 200; i++) {
set_alloc_failure_countdown_to(i);
index_t * index = index_build("examples/repeats.fa", "test_base20");
index_free(index);
}
reset_alloc();
unredirect_stderr();
}
void
test_mem_index_ann_new
(void)
{
redirect_stderr();
index_t * index = index_build("examples/repeats.fa", "test_base20");
test_assert_critical(index != NULL);
// Set alloc failure rate to 0.1.
set_alloc_failure_rate_to(0.1);
for (int i = 0; i < 1000; i++) {
if (index_ann_new(25, 1, 1, index) == 0) {
unlink("test_base20.ann.25.1");
ann_free(index->ann[0]);
free(index->ann);
index->ann = NULL;
index->ann_cnt = 0;
}
}
reset_alloc();
// Set alloc countdown 0->10.
for (int i = 0; i <= 1000; i++) {
set_alloc_failure_countdown_to(i);
if (index_ann_new(25, 1, 1, index) == 0) {
unlink("test_base20.ann.25.1");
ann_free(index->ann[0]);
free(index->ann);
index->ann = NULL;
index->ann_cnt = 0;
}
}
reset_alloc();
index_free(index);
unredirect_stderr();
}
void
test_new_histo
(void)
{
histo_t *histo;
histo = new_histo();
test_assert_critical(histo != NULL);
for (size_t i = 0 ; i < HISTO_INIT_SIZE ; i++) {
test_assert(histo->num[i] == 0);
}
free(histo);
redirect_stderr();
set_alloc_failure_rate_to(1.0);
histo = new_histo();
reset_alloc();
unredirect_stderr();
test_assert(histo == NULL);
test_assert(strcmp(caught_in_stderr(), "") != 0);
return;
}
void
assert_fail_non_critical
(
const char * assertion,
const char * file,
const unsigned int lineno,
const char * function
)
{
TEST_CASE_FAILED = 1;
if (++N_ERROR_MESSAGES > MAX_N_ERROR_MESSAGES + 1) return;
int switch_stderr = STDERR_OFF;
if (switch_stderr) unredirect_stderr();
if (N_ERROR_MESSAGES == MAX_N_ERROR_MESSAGES + 1) {
fprintf(stderr, "more than %d failed assertions...\n",
MAX_N_ERROR_MESSAGES);
}
else {
fprintf(stderr, "assertion failed in %s(), %s:%d: `%s'\n",
function, file, lineno, assertion);
}
fflush(stderr);
if (switch_stderr) redirect_stderr();
}
int
main(
int argc,
char ** argv)
{
int foreground;
int batch;
int redirect;
char **datearg = NULL;
int nb_datearg = 0;
char *conf_diskfile;
char *conf_tapelist;
char *conf_logfile;
int conf_usetimestamps;
disklist_t diskq;
disk_t *dp;
pid_t pid;
pid_t driver_pid, reporter_pid;
amwait_t exitcode;
int opt;
GSList *holding_list=NULL, *holding_file;
int driver_pipe[2];
char date_string[100];
char date_string_standard[100];
time_t today;
char *errstr;
struct tm *tm;
char *tapedev;
char *tpchanger;
char *qdisk, *qhname;
GSList *datestamp_list = NULL;
config_overrides_t *cfg_ovr;
char **config_options;
find_result_t *holding_files;
disklist_t holding_disklist = { NULL, NULL };
/*
* Configure program for internationalization:
* 1) Only set the message locale for now.
* 2) Set textdomain for all amanda related programs to "amanda"
* We don't want to be forced to support dozens of message catalogs.
*/
setlocale(LC_MESSAGES, "C");
textdomain("amanda");
safe_fd(-1, 0);
safe_cd();
set_pname("amflush");
/* Don't die when child closes pipe */
signal(SIGPIPE, SIG_IGN);
dbopen(DBG_SUBDIR_SERVER);
add_amanda_log_handler(amanda_log_stderr);
foreground = 0;
batch = 0;
redirect = 1;
/* process arguments */
cfg_ovr = new_config_overrides(argc/2);
while((opt = getopt(argc, argv, "bfso:D:")) != EOF) {
switch(opt) {
case 'b': batch = 1;
break;
case 'f': foreground = 1;
break;
case 's': redirect = 0;
break;
case 'o': add_config_override_opt(cfg_ovr, optarg);
break;
case 'D': if (datearg == NULL)
datearg = g_malloc(21*sizeof(char *));
if(nb_datearg == 20) {
g_fprintf(stderr,_("maximum of 20 -D arguments.\n"));
exit(1);
}
datearg[nb_datearg++] = g_strdup(optarg);
datearg[nb_datearg] = NULL;
break;
}
}
argc -= optind, argv += optind;
if(!foreground && !redirect) {
g_fprintf(stderr,_("Can't redirect to stdout/stderr if not in forground.\n"));
exit(1);
}
if(argc < 1) {
error(_("Usage: amflush [-b] [-f] [-s] [-D date]* [-o configoption]* <confdir> [host [disk]* ]*"));
/*NOTREACHED*/
}
set_config_overrides(cfg_ovr);
config_init(CONFIG_INIT_EXPLICIT_NAME,
argv[0]);
conf_diskfile = config_dir_relative(getconf_str(CNF_DISKFILE));
read_diskfile(conf_diskfile, &diskq);
amfree(conf_diskfile);
if (config_errors(NULL) >= CFGERR_WARNINGS) {
config_print_errors();
if (config_errors(NULL) >= CFGERR_ERRORS) {
g_critical(_("errors processing config file"));
}
}
check_running_as(RUNNING_AS_DUMPUSER);
dbrename(get_config_name(), DBG_SUBDIR_SERVER);
/* load DLEs from the holding disk, in case there's anything to flush there */
search_holding_disk(&holding_files, &holding_disklist);
/* note that the dumps are added to the global disklist, so we need not
* consult holding_files or holding_disklist after this. The holding-only
* dumps will be filtered properly by match_disklist, setting the dp->todo
* flag appropriately. */
errstr = match_disklist(&diskq, argc-1, argv+1);
if (errstr) {
g_printf(_("%s"),errstr);
amfree(errstr);
}
conf_tapelist = config_dir_relative(getconf_str(CNF_TAPELIST));
if(read_tapelist(conf_tapelist)) {
error(_("could not load tapelist \"%s\""), conf_tapelist);
/*NOTREACHED*/
}
amfree(conf_tapelist);
conf_usetimestamps = getconf_boolean(CNF_USETIMESTAMPS);
amflush_datestamp = get_datestamp_from_time(0);
if(conf_usetimestamps == 0) {
amflush_timestamp = g_strdup(amflush_datestamp);
}
else {
amflush_timestamp = get_timestamp_from_time(0);
}
conf_logdir = config_dir_relative(getconf_str(CNF_LOGDIR));
conf_logfile = g_strjoin(NULL, conf_logdir, "/log", NULL);
if (access(conf_logfile, F_OK) == 0) {
run_amcleanup(get_config_name());
}
if (access(conf_logfile, F_OK) == 0) {
char *process_name = get_master_process(conf_logfile);
error(_("%s exists: %s is already running, or you must run amcleanup"), conf_logfile, process_name);
/*NOTREACHED*/
}
driver_program = g_strjoin(NULL, amlibexecdir, "/", "driver", NULL);
reporter_program = g_strjoin(NULL, sbindir, "/", "amreport", NULL);
logroll_program = g_strjoin(NULL, amlibexecdir, "/", "amlogroll", NULL);
tapedev = getconf_str(CNF_TAPEDEV);
tpchanger = getconf_str(CNF_TPCHANGER);
if (tapedev == NULL && tpchanger == NULL) {
error(_("No tapedev or tpchanger specified"));
}
/* if dates were specified (-D), then use match_datestamp
* against the list of all datestamps to turn that list
* into a set of existing datestamps (basically, evaluate the
* expressions into actual datestamps) */
if(datearg) {
GSList *all_datestamps;
GSList *datestamp;
int i, ok;
all_datestamps = holding_get_all_datestamps();
for(datestamp = all_datestamps; datestamp != NULL; datestamp = datestamp->next) {
ok = 0;
for(i=0; i<nb_datearg && ok==0; i++) {
ok = match_datestamp(datearg[i], (char *)datestamp->data);
}
if (ok)
datestamp_list = g_slist_insert_sorted(datestamp_list,
g_strdup((char *)datestamp->data),
g_compare_strings);
}
slist_free_full(all_datestamps, g_free);
}
else {
/* otherwise, in batch mode, use all datestamps */
if(batch) {
datestamp_list = holding_get_all_datestamps();
}
/* or allow the user to pick datestamps */
else {
datestamp_list = pick_datestamp();
}
}
if(!datestamp_list) {
g_printf(_("Could not find any Amanda directories to flush.\n"));
exit(1);
}
holding_list = holding_get_files_for_flush(datestamp_list);
if (holding_list == NULL) {
g_printf(_("Could not find any valid dump image, check directory.\n"));
exit(1);
}
if (access(conf_logfile, F_OK) == 0) {
char *process_name = get_master_process(conf_logfile);
error(_("%s exists: someone started %s"), conf_logfile, process_name);
/*NOTREACHED*/
}
log_add(L_INFO, "%s pid %ld", get_pname(), (long)getpid());
if(!batch) confirm(datestamp_list);
for(dp = diskq.head; dp != NULL; dp = dp->next) {
if(dp->todo) {
char *qname;
qname = quote_string(dp->name);
log_add(L_DISK, "%s %s", dp->host->hostname, qname);
amfree(qname);
}
}
if(!foreground) { /* write it before redirecting stdout */
puts(_("Running in background, you can log off now."));
puts(_("You'll get mail when amflush is finished."));
}
if(redirect) redirect_stderr();
if(!foreground) detach();
add_amanda_log_handler(amanda_log_stderr);
add_amanda_log_handler(amanda_log_trace_log);
today = time(NULL);
tm = localtime(&today);
if (tm) {
strftime(date_string, 100, "%a %b %e %H:%M:%S %Z %Y", tm);
strftime(date_string_standard, 100, "%Y-%m-%d %H:%M:%S %Z", tm);
} else {
error(_("BAD DATE")); /* should never happen */
}
g_fprintf(stderr, _("amflush: start at %s\n"), date_string);
g_fprintf(stderr, _("amflush: datestamp %s\n"), amflush_timestamp);
g_fprintf(stderr, _("amflush: starttime %s\n"), amflush_timestamp);
g_fprintf(stderr, _("amflush: starttime-locale-independent %s\n"),
date_string_standard);
log_add(L_START, _("date %s"), amflush_timestamp);
/* START DRIVER */
if(pipe(driver_pipe) == -1) {
error(_("error [opening pipe to driver: %s]"), strerror(errno));
/*NOTREACHED*/
}
if((driver_pid = fork()) == 0) {
/*
* This is the child process.
*/
dup2(driver_pipe[0], 0);
close(driver_pipe[1]);
config_options = get_config_options(3);
config_options[0] = "driver";
config_options[1] = get_config_name();
config_options[2] = "nodump";
safe_fd(-1, 0);
execve(driver_program, config_options, safe_env());
error(_("cannot exec %s: %s"), driver_program, strerror(errno));
/*NOTREACHED*/
} else if(driver_pid == -1) {
error(_("cannot fork for %s: %s"), driver_program, strerror(errno));
/*NOTREACHED*/
}
driver_stream = fdopen(driver_pipe[1], "w");
if (!driver_stream) {
error(_("Can't fdopen: %s"), strerror(errno));
/*NOTREACHED*/
}
g_fprintf(driver_stream, "DATE %s\n", amflush_timestamp);
for(holding_file=holding_list; holding_file != NULL;
holding_file = holding_file->next) {
dumpfile_t file;
holding_file_get_dumpfile((char *)holding_file->data, &file);
if (holding_file_size((char *)holding_file->data, 1) <= 0) {
g_debug("%s is empty - ignoring", (char *)holding_file->data);
log_add(L_INFO, "%s: removing file with no data.",
(char *)holding_file->data);
holding_file_unlink((char *)holding_file->data);
dumpfile_free_data(&file);
continue;
}
/* search_holding_disk should have already ensured that every
* holding dumpfile has an entry in the dynamic disklist */
dp = lookup_disk(file.name, file.disk);
assert(dp != NULL);
/* but match_disklist may have indicated we should not flush it */
if (dp->todo == 0) continue;
qdisk = quote_string(file.disk);
qhname = quote_string((char *)holding_file->data);
g_fprintf(stderr,
"FLUSH %s %s %s %d %s\n",
file.name,
qdisk,
file.datestamp,
file.dumplevel,
qhname);
g_debug("flushing '%s'", (char *)holding_file->data);
g_fprintf(driver_stream,
"FLUSH %s %s %s %d %s\n",
file.name,
qdisk,
file.datestamp,
file.dumplevel,
qhname);
amfree(qdisk);
amfree(qhname);
dumpfile_free_data(&file);
}
g_fprintf(stderr, "ENDFLUSH\n"); fflush(stderr);
g_fprintf(driver_stream, "ENDFLUSH\n"); fflush(driver_stream);
fclose(driver_stream);
/* WAIT DRIVER */
while(1) {
if((pid = wait(&exitcode)) == -1) {
if(errno == EINTR) {
continue;
} else {
error(_("wait for %s: %s"), driver_program, strerror(errno));
/*NOTREACHED*/
}
} else if (pid == driver_pid) {
break;
}
}
slist_free_full(datestamp_list, g_free);
datestamp_list = NULL;
slist_free_full(holding_list, g_free);
holding_list = NULL;
if(redirect) { /* rename errfile */
char *errfile, *errfilex, *nerrfilex, number[100];
int tapecycle;
int maxdays, days;
struct stat stat_buf;
errfile = g_strjoin(NULL, conf_logdir, "/amflush", NULL);
errfilex = NULL;
nerrfilex = NULL;
tapecycle = getconf_int(CNF_TAPECYCLE);
maxdays = tapecycle + 2;
days = 1;
/* First, find out the last existing errfile, */
/* to avoid ``infinite'' loops if tapecycle is infinite */
g_snprintf(number,100,"%d",days);
errfilex = newvstralloc(errfilex, errfile, ".", number, NULL);
while ( days < maxdays && stat(errfilex,&stat_buf)==0) {
days++;
g_snprintf(number,100,"%d",days);
errfilex = newvstralloc(errfilex, errfile, ".", number, NULL);
}
g_snprintf(number,100,"%d",days);
errfilex = newvstralloc(errfilex, errfile, ".", number, NULL);
nerrfilex = NULL;
while (days > 1) {
amfree(nerrfilex);
nerrfilex = errfilex;
days--;
g_snprintf(number,100,"%d",days);
errfilex = g_strjoin(NULL, errfile, ".", number, NULL);
if (rename(errfilex, nerrfilex) != 0) {
error(_("cannot rename \"%s\" to \"%s\": %s"),
errfilex, nerrfilex, strerror(errno));
/*NOTREACHED*/
}
}
errfilex = newvstralloc(errfilex, errfile, ".1", NULL);
if (rename(errfile,errfilex) != 0) {
error(_("cannot rename \"%s\" to \"%s\": %s"),
errfilex, nerrfilex, strerror(errno));
/*NOTREACHED*/
}
amfree(errfile);
amfree(errfilex);
amfree(nerrfilex);
}
/*
* Have amreport generate report and send mail. Note that we do
* not bother checking the exit status. If it does not work, it
* can be rerun.
*/
if((reporter_pid = fork()) == 0) {
/*
* This is the child process.
*/
config_options = get_config_options(3);
config_options[0] = "amreport";
config_options[1] = get_config_name();
config_options[2] = "--from-amdump";
safe_fd(-1, 0);
execve(reporter_program, config_options, safe_env());
error(_("cannot exec %s: %s"), reporter_program, strerror(errno));
/*NOTREACHED*/
} else if(reporter_pid == -1) {
error(_("cannot fork for %s: %s"), reporter_program, strerror(errno));
/*NOTREACHED*/
}
while(1) {
if((pid = wait(&exitcode)) == -1) {
if(errno == EINTR) {
continue;
} else {
error(_("wait for %s: %s"), reporter_program, strerror(errno));
/*NOTREACHED*/
}
} else if (pid == reporter_pid) {
break;
}
}
log_add(L_INFO, "pid-done %ld", (long)getpid());
/*
* Call amlogroll to rename the log file to its datestamped version.
* Since we exec at this point, our exit code will be that of amlogroll.
*/
config_options = get_config_options(2);
config_options[0] = "amlogroll";
config_options[1] = get_config_name();
safe_fd(-1, 0);
execve(logroll_program, config_options, safe_env());
error(_("cannot exec %s: %s"), logroll_program, strerror(errno));
/*NOTREACHED*/
return 0; /* keep the compiler happy */
}
void
test_io_stream_read_seq
(void)
{
iostream_t * stream;
gstack_t * stack;
seqread_t * read;
// Invalid arguments.
redirect_stderr();
test_assert(io_stream_read_seq(NULL) == NULL);
unredirect_stderr();
// Load files.
// Read RAW file.
stream = io_stream_open("examples/io_input.raw");
test_assert_critical(stream != NULL);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 6);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "NNNNNNLLYYYYJDFLS") == 0);
test_assert(strcmp(seqread_tag(read), "6") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "NNNNNNNNACGTACGCC") == 0);
test_assert(strcmp(seqread_tag(read), "5") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "ACGTACATGTATGACAC") == 0);
test_assert(strcmp(seqread_tag(read), "4") == 0);
seqread_free(read);
gstack_free(stack);
io_stream_free(stream);
// Read FASTA file.
stream = io_stream_open_buf("examples/io_input.fasta", 80);
test_assert_critical(stream != NULL);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 4);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "ACGTACATGTATGACAC") == 0);
test_assert(strcmp(seqread_tag(read), "seq4") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "AGTCGANTATACNTACG") == 0);
test_assert(strcmp(seqread_tag(read), "seq3") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "GTATCGACTACGAGCTA") == 0);
test_assert(strcmp(seqread_tag(read), "seq2") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "ATGCGTACGTCGTATCA") == 0);
test_assert(strcmp(seqread_tag(read), "seq1") == 0);
seqread_free(read);
gstack_free(stack);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 2);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "NNNNNNLLYYYYJDFLS") == 0);
test_assert(strcmp(seqread_tag(read), "seq6") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "NNNNNNNNACGTACGCC") == 0);
test_assert(strcmp(seqread_tag(read), "seq5") == 0);
seqread_free(read);
gstack_free(stack);
io_stream_free(stream);
// Read FASTQ file.
stream = io_stream_open_buf("examples/io_input.fastq", 50);
test_assert_critical(stream != NULL);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 2);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "GTATCGACTACGAGCTA") == 0);
test_assert(strcmp(seqread_tag(read), "seq2") == 0);
test_assert(strcmp(seqread_qscore(read), "BACBABCA0ACBB00AC") == 0);
seqread_free(read);
read = seqread_pop(stack);
test_assert(read != NULL);
test_assert(strcmp(seqread_seq(read), "ATGCGTACGTCGTATCA") == 0);
test_assert(strcmp(seqread_tag(read), "seq1") == 0);
test_assert(strcmp(seqread_qscore(read), "12391284194819241") == 0);
seqread_free(read);
gstack_free(stack);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 2);
gstack_free(stack);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 2);
gstack_free(stack);
stack = io_stream_read_seq(stream);
test_assert_critical(stack != NULL);
test_assert(gstack_num_elm(stack) == 0);
gstack_free(stack);
stack = io_stream_read_seq(stream);
test_assert(stack == NULL);
io_stream_free(stream);
}
