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Merge pull request #24 from jeromekelleher/buffer-safety-3
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Buffer safety and refactoring
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@jeromekelleher
jeromekelleher authored Jul 12, 2024
2 parents 5c35fa6 + e65fa4c commit dd9ccbc
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Showing 3 changed files with 218 additions and 118 deletions.
112 changes: 85 additions & 27 deletions lib/tests.c
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ test_int_field_1d(void)
.num_columns = 1,
.data = (const char *) data };
char buf[1000];
const char *expected[] = { "1\t", "2\t", "12345789\t", ".\t", "-100\t" };
const char *expected[] = { "1", "2", "12345789", ".", "-100" };
int64_t ret;
size_t j;

Expand All @@ -43,15 +43,15 @@ test_int_field_1d_overflow(void)
.item_size = 4,
.num_columns = 1,
.data = (const char *) data };
int64_t ret;
size_t j, buflen;
int64_t ret, buflen;
size_t j;
char *buf;

for (j = 0; j < num_rows - 1; j++) {
/* printf("%d\n", (int) data[j]); */
for (buflen = 0; buflen <= VCZ_INT32_BUF_SIZE; buflen++) {
/* printf("buflen = %d\n", (int) buflen); */
buf = malloc(buflen);
buf = malloc((size_t) buflen);
CU_ASSERT_FATAL(buf != NULL);
ret = vcz_field_write(&field, j, buf, buflen, 0);
free(buf);
Expand All @@ -60,9 +60,9 @@ test_int_field_1d_overflow(void)
}
j = num_rows - 1;
CU_ASSERT_FATAL(data[j] == -1);
/* Missing data is treated differently. Just need 2 bytes for ".\t" */
for (buflen = 0; buflen < 2; buflen++) {
buf = malloc(buflen);
/* Missing data is treated differently. Just need 1 byte for "." */
for (buflen = 0; buflen < 1; buflen++) {
buf = malloc((size_t) buflen);
CU_ASSERT_FATAL(buf != NULL);
ret = vcz_field_write(&field, j, buf, buflen, 0);
free(buf);
Expand All @@ -81,7 +81,7 @@ test_int_field_2d(void)
.num_columns = 3,
.data = (const char *) data };
char buf[1000];
const char *expected[] = { "1,2,3\t", "1234,5678\t", ".\t", "\t" };
const char *expected[] = { "1,2,3", "1234,5678", ".", "" };
int64_t ret;
size_t j;

Expand All @@ -106,7 +106,7 @@ test_float_field_1d(void)
.data = (const char *) data };
char buf[1000];
const char *expected[]
= { "1\t", "2.1\t", "-2147483648\t", "12345789\t", "-1\t", "-100.123\t", ".\t" };
= { "1", "2.1", "-2147483648", "12345789", "-1", "-100.123", "." };
int64_t ret;
size_t j;
int32_t *int_data = (int32_t *) data;
Expand All @@ -115,8 +115,8 @@ test_float_field_1d(void)

for (j = 0; j < num_rows; j++) {
ret = vcz_field_write(&field, j, buf, 1000, 0);
printf("ret = %d\n", (int)ret);
printf("'%.*s':'%s'\n", (int) ret, buf, expected[j]);
/* printf("ret = %d\n", (int)ret); */
/* printf("'%.*s':'%s'\n", (int) ret, buf, expected[j]); */
CU_ASSERT_EQUAL_FATAL(ret, strlen(expected[j]));
CU_ASSERT_NSTRING_EQUAL(buf, expected[j], ret);
}
Expand All @@ -132,8 +132,8 @@ test_float_field_1d_overflow(void)
.item_size = 4,
.num_columns = 1,
.data = (const char *) data };
int64_t ret;
size_t j, buflen;
int64_t ret, buflen;
size_t j;
char *buf;
int32_t *int_data = (int32_t *) data;

Expand All @@ -143,17 +143,17 @@ test_float_field_1d_overflow(void)
/* printf("%d\n", (int) data[j]); */
for (buflen = 0; buflen <= VCZ_FLOAT32_BUF_SIZE; buflen++) {
/* printf("buflen = %d\n", (int) buflen); */
buf = malloc(buflen);
buf = malloc((size_t) buflen);
CU_ASSERT_FATAL(buf != NULL);
ret = vcz_field_write(&field, j, buf, buflen, 0);
free(buf);
CU_ASSERT_FATAL(ret == VCZ_ERR_BUFFER_OVERFLOW);
}
}
j = num_rows - 1;
/* Missing data is treated differently. Just need 2 bytes for ".\t" */
for (buflen = 0; buflen < 2; buflen++) {
buf = malloc(buflen);
/* Missing data is treated differently. Just need 1 byte for "." */
for (buflen = 0; buflen < 1; buflen++) {
buf = malloc((size_t) buflen);
CU_ASSERT_FATAL(buf != NULL);
ret = vcz_field_write(&field, j, buf, buflen, 0);
free(buf);
Expand All @@ -176,15 +176,59 @@ test_string_field_1d(void)
.num_columns = 1,
.data = data };
char buf[1000];
const char *expected[] = { "X\t", "XX\t", "XXX\t" };
const char *expected[] = { "X", "XX", "XXX" };
int64_t ret;
size_t j;

CU_ASSERT_EQUAL_FATAL(sizeof(data), 10);
for (j = 0; j < num_rows; j++) {
ret = vcz_field_write(&field, j, buf, 1000, 0);
CU_ASSERT_EQUAL_FATAL(ret, strlen(expected[j]));
CU_ASSERT_STRING_EQUAL(buf, expected[j]);
CU_ASSERT_NSTRING_EQUAL(buf, expected[j], ret);
}
}

static void
test_string_field_1d_overflow(void)
{
/* item_size=4, rows=3, cols=1 */
const size_t num_rows = 4;
const size_t item_size = 3;
const char data[] = "X\0\0" /* X */
"XX\0" /* XX*/
"XXX" /* XXX, */
".\0\0"; /* . */
vcz_field_t field = { .name = "test",
.type = VCZ_TYPE_STRING,
.item_size = 3,
.num_columns = 1,
.data = data };
int64_t ret, buflen;
size_t j;
char *buf;

for (j = 0; j < num_rows - 1; j++) {
for (buflen = 0; buflen < (int) item_size; buflen++) {
/* printf("buflen = %d\n", (int) buflen); */
buf = malloc((size_t) buflen);
CU_ASSERT_FATAL(buf != NULL);
ret = vcz_field_write(&field, j, buf, buflen, 0);
free(buf);
if (ret < 0) {
CU_ASSERT_FATAL(ret == VCZ_ERR_BUFFER_OVERFLOW);
} else {
CU_ASSERT_EQUAL_FATAL(ret, j + 1);
}
}
}
j = num_rows - 1;
/* Missing data is treated differently. Just need 1 byte for "." */
for (buflen = 0; buflen < 1; buflen++) {
buf = malloc((size_t) buflen);
CU_ASSERT_FATAL(buf != NULL);
ret = vcz_field_write(&field, j, buf, buflen, 0);
free(buf);
CU_ASSERT_FATAL(ret == VCZ_ERR_BUFFER_OVERFLOW);
}
}

Expand All @@ -196,14 +240,13 @@ test_string_field_2d(void)
const char data[] = "X\0\0Y\0\0\0\0\0" /* [X, Y] */
"XX\0YY\0Z\0\0" /* [XX, YY, Z], */
"XXX\0\0\0\0\0"; /* [XXX], */

vcz_field_t field = { .name = "test",
.type = VCZ_TYPE_STRING,
.item_size = 3,
.num_columns = 3,
.data = data };
char buf[1000];
const char *expected[] = { "X,Y\t", "XX,YY,Z\t", "XXX\t" };
const char *expected[] = { "X,Y", "XX,YY,Z", "XXX" };
int64_t ret;
size_t j;

Expand All @@ -212,7 +255,7 @@ test_string_field_2d(void)
for (j = 0; j < num_rows; j++) {
ret = vcz_field_write(&field, j, buf, 1000, 0);
CU_ASSERT_EQUAL_FATAL(ret, strlen(expected[j]));
CU_ASSERT_STRING_EQUAL(buf, expected[j]);
CU_ASSERT_NSTRING_EQUAL(buf, expected[j], ret);
}
}

Expand All @@ -237,13 +280,13 @@ test_variant_encoder_minimal(void)
const int32_t hq_data[] = { 10, 15, 7, 12, -1, -1, -1, -1 };
const float gl_data[] = { 1, 2, 3, 4, 1.1f, 1.2f, 1.3f, 1.4f };
int64_t ret;
size_t j;
size_t j, buflen;
vcz_variant_encoder_t writer;
const char *expected[] = {
"X\t123\tRS1\tA\tT\t9\tPASS\tAA=G\tGT:HQ:GL\t0/0:10,15:1,2\t0|1:7,12:3,4",
"YY\t45678\tRS2\tG\t.\t12.1\tFILT1\tAN=9;FLAG\tGT:GL\t1|1:1.1,1.2\t1/0:1.3,1.4",
};
char buf[1000];
char *buf;

ret = vcz_variant_encoder_init(&writer, 2, 2, contig_data, 2, pos_data, id_data, 3,
1, ref_data, 1, alt_data, 1, 1, qual_data, filter_id_data, 5, 2, filter_data);
Expand All @@ -270,14 +313,27 @@ test_variant_encoder_minimal(void)
/* vcz_variant_encoder_print_state(&writer, stdout); */

for (j = 0; j < num_rows; j++) {
ret = vcz_variant_encoder_write_row(&writer, j, buf, 1000);
/* printf("ret = %d\n", ret); */
for (buflen = 0;; buflen++) {
/* printf("buflen = %d\n", (int) buflen); */
buf = malloc(buflen);
CU_ASSERT_FATAL(buf != NULL);
ret = vcz_variant_encoder_write_row(&writer, j, buf, buflen);
if (ret < 0) {
free(buf);
CU_ASSERT_EQUAL_FATAL(ret, VCZ_ERR_BUFFER_OVERFLOW);
} else {
break;
}
}
CU_ASSERT_FATAL(buflen >= strlen(expected[j]));
/* printf("ret = %d\n", (int) ret); */
/* printf("GOT:%s\n", buf); */
/* printf("EXP:%s\n", expected[j]); */
/* printf("GOT:%d\n", (int) strlen(buf)); */
/* printf("EXP:%d\n", (int) strlen(expected[j])); */
CU_ASSERT_EQUAL(ret, strlen(expected[j]));
CU_ASSERT_STRING_EQUAL(buf, expected[j]);
free(buf);
}
vcz_variant_encoder_free(&writer);
}
Expand Down Expand Up @@ -460,7 +516,8 @@ test_ftoa(void)

for (j = 0; j < sizeof(cases) / sizeof(*cases); j++) {
len = vcz_ftoa(buf, cases[j].val);
/* printf("j = %d %f->%s=='%s'\n", (int) j, cases[j].val, cases[j].expected, buf); */
/* printf("j = %d %f->%s=='%s'\n", (int) j, cases[j].val, cases[j].expected,
* buf); */
CU_ASSERT_EQUAL_FATAL(len, strlen(cases[j].expected));
CU_ASSERT_STRING_EQUAL_FATAL(buf, cases[j].expected);
}
Expand Down Expand Up @@ -553,6 +610,7 @@ main(int argc, char **argv)
{
CU_TestInfo tests[] = {
{ "test_string_field_1d", test_string_field_1d },
{ "test_string_field_1d_overflow", test_string_field_1d_overflow },
{ "test_string_field_2d", test_string_field_2d },
{ "test_int_field_1d", test_int_field_1d },
{ "test_int_field_1d_overflow", test_int_field_1d_overflow },
Expand Down
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