void testCactusDisk_getUniqueID_UniqueIntervals(CuTest* testCase) {
cactusDiskTestSetup();
stSortedSet *uniqueNames = stSortedSet_construct3(testCactusDisk_getUniqueID_UniqueP, free);
for (int64_t i = 0; i < 10; i++) { //Gets a billion ids, checks we are good.
int64_t intervalSize = st_randomInt(0, 100000);
Name uniqueName = cactusDisk_getUniqueIDInterval(cactusDisk, intervalSize);
for(int64_t j=0; j<intervalSize; j++) {
CuAssertTrue(testCase, uniqueName > 0);
CuAssertTrue(testCase, uniqueName < INT64_MAX);
CuAssertTrue(testCase, uniqueName != NULL_NAME);
char *cA = cactusMisc_nameToString(uniqueName);
CuAssertTrue(testCase, stSortedSet_search(uniqueNames, cA) == NULL);
CuAssertTrue(testCase, cactusMisc_stringToName(cA) == uniqueName);
stSortedSet_insert(uniqueNames, cA);
uniqueName++;
}
}
stSortedSet_destruct(uniqueNames);
cactusDiskTestTeardown();
}
Name cactusDisk_addString(CactusDisk *cactusDisk, const char *string) {
/*
* Adds a string to the database.
*/
if (cactusDisk->storeSequencesInAFile) {
if (cactusDisk->sequencesWriteFileHandle == NULL) {
//We do not allow the read file handle to be open at the same time.
if (cactusDisk->sequencesReadFileHandle != NULL) {
fclose(cactusDisk->sequencesReadFileHandle);
cactusDisk->sequencesReadFileHandle = NULL;
}
cactusDisk->sequencesWriteFileHandle = fopen(cactusDisk->absSequencesFileName, "a");
assert(cactusDisk->sequencesWriteFileHandle != NULL);
}
else {
//The read file handle should not be open at the same time.
assert(cactusDisk->sequencesReadFileHandle == NULL);
}
Name name = ftell(cactusDisk->sequencesWriteFileHandle) + 1;
//Extra temporary cheesy code to avoid potential overflow in fprintf
int64_t chunkSize = 1000000000; //1 gig approx chunks, to avoid a possible overflow issue with fprintf
int64_t length = strlen(string);
if (length > chunkSize) {
fprintf(cactusDisk->sequencesWriteFileHandle, ">");
for (int64_t i = 0; i < length;) {
int64_t j = i + chunkSize <= length ? chunkSize : length - i;
char *string2 = memcpy(st_malloc(sizeof(char) * (j + 1)), string + i, sizeof(char) * j);
string2[j] = '\0';
int64_t k = fprintf(cactusDisk->sequencesWriteFileHandle, "%s", string2);
(void) k;
assert(k == j);
free(string2);
i += j;
}
} else {
//Replacing this line
int64_t k = fprintf(cactusDisk->sequencesWriteFileHandle, ">%s", string);
(void) k;
assert(k == length + 1);
}
#ifndef NDEBUG
// Extra fsync may not be necessary.
fsync(fileno(cactusDisk->sequencesWriteFileHandle));
fclose(cactusDisk->sequencesWriteFileHandle);
cactusDisk->sequencesWriteFileHandle = NULL;
cactusDisk->sequencesReadFileHandle = fopen(cactusDisk->absSequencesFileName, "r");
char *string2 = getStringFromDisk(cactusDisk->sequencesReadFileHandle, name, 0, length);
for (int64_t i = 0; i < length; i++) {
assert(string[i] == string2[i]);
}
free(string2);
#endif
return name;
} else {
int64_t stringSize = strlen(string);
int64_t intervalSize = ceil((double) stringSize / CACTUS_DISK_SEQUENCE_CHUNK_SIZE);
Name name = cactusDisk_getUniqueIDInterval(cactusDisk, intervalSize);
stList *insertRequests = stList_construct3(0, (void (*)(void *)) stKVDatabaseBulkRequest_destruct);
for (int64_t i = 0; i * CACTUS_DISK_SEQUENCE_CHUNK_SIZE < stringSize; i++) {
int64_t j =
(i + 1) * CACTUS_DISK_SEQUENCE_CHUNK_SIZE < stringSize ?
CACTUS_DISK_SEQUENCE_CHUNK_SIZE : stringSize - i * CACTUS_DISK_SEQUENCE_CHUNK_SIZE;
char *subString = stString_getSubString(string, i * CACTUS_DISK_SEQUENCE_CHUNK_SIZE, j);
stList_append(insertRequests, stKVDatabaseBulkRequest_constructInsertRequest(name + i, subString, j + 1));
free(subString);
}
stTry
{
stKVDatabase_bulkSetRecords(cactusDisk->database, insertRequests);
}
stCatch(except)
{
stThrowNewCause(except, ST_KV_DATABASE_EXCEPTION_ID,
"An unknown database error occurred when we tried to add a string to the cactus disk");
}stTryEnd
;
stList_destruct(insertRequests);
return name;
}
}
