static void setRecord(stKVDatabase *database, int64_t key,
const void *value, int64_t sizeOfRecord) {
if (containsRecord(database, key)) {
updateRecord(database, key, value, sizeOfRecord);
} else {
insertRecord(database, key, value, sizeOfRecord);
}
}
void cactusDisk_addUpdateRequest(CactusDisk *cactusDisk, Flower *flower) {
int64_t recordSize;
void *vA = binaryRepresentation_makeBinaryRepresentation(flower,
(void (*)(void *, void (*)(const void * ptr, size_t size, size_t count))) flower_writeBinaryRepresentation,
&recordSize);
//Compression
vA = compress(vA, &recordSize);
if (containsRecord(cactusDisk, flower_getName(flower))) {
int64_t recordSize2;
void *vA2 = stCache_getRecord(cactusDisk->cache, flower_getName(flower), 0, INT64_MAX, &recordSize2);
if (!stCache_recordsIdentical(vA, recordSize, vA2, recordSize2)) { //Only rewrite if we actually did something
stList_append(cactusDisk->updateRequests,
stKVDatabaseBulkRequest_constructUpdateRequest(flower_getName(flower), vA, recordSize));
}
free(vA2);
} else {
stList_append(cactusDisk->updateRequests,
stKVDatabaseBulkRequest_constructInsertRequest(flower_getName(flower), vA, recordSize));
}
free(vA);
}
void cactusDisk_write(CactusDisk *cactusDisk) {
Flower *flower;
int64_t recordSize;
stList *removeRequests = stList_construct3(0, (void (*)(void *)) stIntTuple_destruct);
st_logDebug("Starting to write the cactus to disk\n");
stSortedSetIterator *it = stSortedSet_getIterator(cactusDisk->flowers);
//Sort flowers to update.
while ((flower = stSortedSet_getNext(it)) != NULL) {
cactusDisk_addUpdateRequest(cactusDisk, flower);
}
stSortedSet_destructIterator(it);
st_logDebug("Got the flowers to update\n");
//Remove nets that are marked for deletion..
it = stSortedSet_getIterator(cactusDisk->flowerNamesMarkedForDeletion);
char *nameString;
while ((nameString = stSortedSet_getNext(it)) != NULL) {
Name name = cactusMisc_stringToName(nameString);
if (containsRecord(cactusDisk, name)) {
stList_append(cactusDisk->updateRequests, stKVDatabaseBulkRequest_constructUpdateRequest(name, &name, 0)); //We set it to null in the first atomic operation.
stList_append(removeRequests, stIntTuple_construct1(name));
}
}
stSortedSet_destructIterator(it);
st_logDebug("Avoided updating nets marked for deletion\n");
// Insert and/or update meta-sequences.
it = stSortedSet_getIterator(cactusDisk->metaSequences);
MetaSequence *metaSequence;
while ((metaSequence = stSortedSet_getNext(it)) != NULL) {
void *vA =
binaryRepresentation_makeBinaryRepresentation(metaSequence,
(void (*)(void *, void (*)(const void * ptr, size_t size, size_t count))) metaSequence_writeBinaryRepresentation,
&recordSize);
//Compression
vA = compress(vA, &recordSize);
if (!containsRecord(cactusDisk, metaSequence_getName(metaSequence))) {
stList_append(cactusDisk->updateRequests,
stKVDatabaseBulkRequest_constructInsertRequest(metaSequence_getName(metaSequence), vA, recordSize));
} else {
stList_append(cactusDisk->updateRequests,
stKVDatabaseBulkRequest_constructUpdateRequest(metaSequence_getName(metaSequence), vA, recordSize));
}
free(vA);
}
stSortedSet_destructIterator(it);
st_logDebug("Got the sequences we are going to add to the database.\n");
if (!containsRecord(cactusDisk, CACTUS_DISK_PARAMETER_KEY)) { //We only write the parameters once.
//Finally the database info.
void *cactusDiskParameters =
binaryRepresentation_makeBinaryRepresentation(cactusDisk,
(void (*)(void *, void (*)(const void * ptr, size_t size, size_t count))) cactusDisk_writeBinaryRepresentation,
&recordSize);
//Compression
cactusDiskParameters = compress(cactusDiskParameters, &recordSize);
stList_append(cactusDisk->updateRequests,
stKVDatabaseBulkRequest_constructInsertRequest(CACTUS_DISK_PARAMETER_KEY, cactusDiskParameters,
recordSize));
free(cactusDiskParameters);
}
st_logDebug("Checked if need to write the initial parameters\n");
if (stList_length(cactusDisk->updateRequests) > 0) {
st_logDebug("Going to write %" PRIi64 " updates\n", stList_length(cactusDisk->updateRequests));
stTry
{
st_logDebug("Writing %" PRIi64 " updates\n", stList_length(cactusDisk->updateRequests));
assert(stList_length(cactusDisk->updateRequests) > 0);
stKVDatabase_bulkSetRecords(cactusDisk->database, cactusDisk->updateRequests);
}
stCatch(except)
{
stThrowNewCause(except, ST_KV_DATABASE_EXCEPTION_ID,
"Failed when trying to set records in updating the cactus disk");
}stTryEnd
;
}
static CactusDisk *cactusDisk_constructPrivate(stKVDatabaseConf *conf, bool create, const char *sequencesFileName) {
//sequencesFileName = NULL; //Disable the ability to store the sequences on disk.
CactusDisk *cactusDisk = st_calloc(1, sizeof(CactusDisk));
//construct lists of in memory objects
cactusDisk->metaSequences = stSortedSet_construct3(cactusDisk_constructMetaSequencesP, NULL);
cactusDisk->flowers = stSortedSet_construct3(cactusDisk_constructFlowersP, NULL);
cactusDisk->flowerNamesMarkedForDeletion = stSortedSet_construct3((int (*)(const void *, const void *)) strcmp,
free);
cactusDisk->updateRequests = stList_construct3(0, (void (*)(void *)) stKVDatabaseBulkRequest_destruct);
//Now open the database
cactusDisk->database = stKVDatabase_construct(conf, create);
cactusDisk->cache = stCache_construct();
cactusDisk->stringCache = stCache_construct();
//initialise the unique ids.
int64_t seed = (clock() << 24) | (time(NULL) << 16) | (getpid() & 65535); //Likely to be unique
st_logDebug("The cactus disk is seeding the random number generator with the value %" PRIi64 "\n", seed);
st_randomSeed(seed);
cactusDisk->uniqueNumber = 0;
cactusDisk->maxUniqueNumber = 0;
//Now load any stuff..
if (containsRecord(cactusDisk, CACTUS_DISK_PARAMETER_KEY)) {
if (create) {
stThrowNew(CACTUS_DISK_EXCEPTION_ID, "Tried to create a cactus disk, but the cactus disk already exists");
}
if (sequencesFileName != NULL) {
stThrowNew(CACTUS_DISK_EXCEPTION_ID,
"A sequences file name is specified, but the cactus disk is not being created");
}
void *record = getRecord(cactusDisk, CACTUS_DISK_PARAMETER_KEY, "cactus_disk parameters");
void *record2 = record;
cactusDisk_loadFromBinaryRepresentation(&record, cactusDisk, conf);
free(record2);
} else {
assert(create);
if (sequencesFileName == NULL) {
cactusDisk->storeSequencesInAFile = 0;
cactusDisk->sequencesFileName = NULL;
cactusDisk->sequencesReadFileHandle = NULL;
cactusDisk->sequencesWriteFileHandle = NULL;
cactusDisk->absSequencesFileName = NULL;
} else {
if (stKVDatabaseConf_getDir(conf) == NULL) {
stThrowNew(CACTUS_DISK_EXCEPTION_ID,
"The database conf does not contain a directory in which the sequence file is to be found!\n");
}
cactusDisk->storeSequencesInAFile = 1;
cactusDisk->sequencesFileName = stString_copy(sequencesFileName);
cactusDisk->absSequencesFileName = stString_print("%s/%s", stKVDatabaseConf_getDir(conf),
cactusDisk->sequencesFileName);
//Make sure the file exists
cactusDisk->sequencesReadFileHandle = fopen(cactusDisk->absSequencesFileName, "w");
assert(cactusDisk->sequencesReadFileHandle != NULL);
fclose(cactusDisk->sequencesReadFileHandle); //Flush it first time.
cactusDisk->sequencesReadFileHandle = NULL;
cactusDisk->sequencesWriteFileHandle = NULL;
}
}
return cactusDisk;
}
