void *
run_test
(
void * data
)
{
// Unpack argument. //
const test_case_t test_case = *(test_case_t *) data;
// -- Initialize -- //
// Register signal handlers. This will allow execution
// to return to main thread in case of crash.
signal(SIGSEGV, terminate_thread);
// Get test name and fixture (test function). //
fixture_t fixture = test_case.fixture;
// Initialize variable, empty buffers... //
test_case_init();
unredirect_stderr();
unredirect_stdout();
// -- Run the test -- //
(*fixture)();
// -- Clean -- //
unredirect_stderr();
unredirect_stdout();
test_case_clean();
return NULL;
}
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
terminate_thread
(
int sig
)
{
unredirect_stderr();
// If test was not failed so far, update display.
if (!TEST_CASE_FAILED) {
update_display_failed();
}
fprintf(stderr, "caught SIGTERM (interrupting)\n");
// Label the test case as failed. //
TEST_CASE_FAILED = 1;
// Clean it all. //
test_case_clean();
// Return to main thread.
pthread_exit(NULL);
}
void
fail_critical
(
const char * assertion,
const char * file,
int lineno,
const char * function
)
// Handle failure of critical (fatal) assert statements.
// Set the test status to failed and update the display
// and print error message.
{
// If test was not failed so far, update display.
if (!TEST_CASE_FAILED) {
update_display_failed();
}
TEST_CASE_FAILED = 1;
// That's the end of the test case. We can
// take back stderr without worries.
unredirect_stderr();
fprintf(stderr, "assertion failed in %s, %s:%d: `%s' (CRITICAL)\n",
function, file, lineno, assertion);
fflush(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
assert_fail_critical
(
const char * assertion,
const char * file,
const unsigned int lineno,
const char * function
)
{
TEST_CASE_FAILED = 1;
unredirect_stderr();
fprintf(stderr, "assertion failed in %s(), %s:%d: `%s' (CRITICAL)\n",
function, file, lineno, assertion);
fflush(stderr);
}
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
terminate_thread
(
int sig
)
{
fprintf(stderr, "caught SIGTERM (interrupting)\n");
// Label the test case as failed. //
TEST_CASE_FAILED = 1;
// Clean it all. //
unredirect_stderr();
test_case_clean();
// Return to main thread.
pthread_exit(NULL);
}
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
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();
}
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
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);
}