void testMetaSequence_serialisation(CuTest* testCase) {
cactusMetaSequenceTestSetup();
int64_t i;
Name name = metaSequence_getName(metaSequence);
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, name) == metaSequence);
void *vA = binaryRepresentation_makeBinaryRepresentation(metaSequence,
(void (*)(void *, void (*)(const void *, size_t, size_t)))metaSequence_writeBinaryRepresentation, &i);
CuAssertTrue(testCase, i > 0);
metaSequence_destruct(metaSequence);
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, name) == NULL);
void *vA2 = vA;
metaSequence = metaSequence_loadFromBinaryRepresentation(&vA2, cactusDisk);
CuAssertTrue(testCase, name == metaSequence_getName(metaSequence));
CuAssertStrEquals(testCase, headerString, metaSequence_getHeader(metaSequence));
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, name) == metaSequence);
cactusDisk_write(cactusDisk);
metaSequence_destruct(metaSequence);
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, name) != NULL);
metaSequence = cactusDisk_getMetaSequence(cactusDisk, name);
nestedTest = 1;
testMetaSequence_getName(testCase);
testMetaSequence_getStart(testCase);
testMetaSequence_getLength(testCase);
testMetaSequence_getEventName(testCase);
testMetaSequence_getString(testCase);
testMetaSequence_getHeader(testCase);
testMetaSequence_isTrivialSequence(testCase);
nestedTest = 0;
cactusMetaSequenceTestTeardown();
}
static int64_t setCoordinates(Flower *flower, MetaSequence *metaSequence, Cap *cap, int64_t coordinate) {
/*
* Sets the coordinates of the reference thread and sets the bases of the actual sequence
* that of the consensus.
*/
Sequence *sequence = flower_getSequence(flower, metaSequence_getName(metaSequence));
if (sequence == NULL) {
sequence = sequence_construct(metaSequence, flower);
}
while (1) {
assert(cap_getStrand(cap));
assert(!cap_getSide(cap));
Cap *adjacentCap = cap_getAdjacency(cap);
assert(adjacentCap != NULL);
assert(cap_getStrand(adjacentCap));
assert(cap_getSide(adjacentCap));
int64_t adjacencyLength = cap_getCoordinate(cap);
assert(adjacencyLength == cap_getCoordinate(adjacentCap));
assert(adjacencyLength != INT64_MAX);
assert(adjacencyLength >= 0);
cap_setCoordinates(cap, coordinate, 1, sequence);
coordinate += adjacencyLength + 1;
cap_setCoordinates(adjacentCap, coordinate, 1, sequence);
//Traverse any block..
if ((cap = cap_getOtherSegmentCap(adjacentCap)) == NULL) {
break;
}
coordinate += segment_getLength(cap_getSegment(adjacentCap)) - 1;
}
return coordinate;
}
void metaSequence_writeBinaryRepresentation(MetaSequence *metaSequence,
void (*writeFn)(const void * ptr, size_t size, size_t count)) {
binaryRepresentation_writeElementType(CODE_META_SEQUENCE, writeFn);
binaryRepresentation_writeName(metaSequence_getName(metaSequence), writeFn);
binaryRepresentation_writeInteger(metaSequence_getStart(metaSequence), writeFn);
binaryRepresentation_writeInteger(metaSequence_getLength(metaSequence), writeFn);
binaryRepresentation_writeName(metaSequence_getEventName(metaSequence), writeFn);
binaryRepresentation_writeName(metaSequence->stringName, writeFn);
binaryRepresentation_writeString(metaSequence_getHeader(metaSequence), writeFn);
binaryRepresentation_writeBool(metaSequence_isTrivialSequence(metaSequence), writeFn);
}
static Segment *getSegment(stSortedSet *sortedSegments, int64_t x, MetaSequence *metaSequence) {
segmentCompareFn_coordinate = x;
segmentCompareFn_metaSequence = metaSequence_getName(metaSequence);
Segment *segment = stSortedSet_searchLessThanOrEqual(sortedSegments,
&segmentCompareFn_coordinate);
assert((void *) segment != &segmentCompareFn_coordinate);
if (segment != NULL) {
if(sequence_getMetaSequence(segment_getSequence(segment)) == metaSequence) {
assert(segment_getStart(segment) <= x);
if (x < segment_getStart(segment) + segment_getLength(segment)) {
return segment;
}
}
}
return NULL;
}
void testCactusDisk_getMetaSequence(CuTest* testCase) {
cactusDiskTestSetup();
MetaSequence *metaSequence = metaSequence_construct(1, 10, "ACTGACTGAG",
"FOO", 10, cactusDisk);
MetaSequence *metaSequence2 = metaSequence_construct(2, 10, "CCCCCCCCCC",
"BAR", 10, cactusDisk);
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, metaSequence_getName(metaSequence)) == metaSequence);
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, metaSequence_getName(metaSequence2)) == metaSequence2);
//now try closing the disk, then reloading it, to see if we get the same result.
Name name1 = metaSequence_getName(metaSequence);
Name name2 = metaSequence_getName(metaSequence2);
cactusDisk_write(cactusDisk);
cactusDisk_destruct(cactusDisk);
cactusDisk = cactusDisk_construct(conf, 0);
metaSequence = cactusDisk_getMetaSequence(cactusDisk, name1);
metaSequence2 = cactusDisk_getMetaSequence(cactusDisk, name2);
CuAssertTrue(testCase, metaSequence != NULL);
CuAssertTrue(testCase, metaSequence2 != NULL);
CuAssertTrue(testCase, metaSequence_getName(metaSequence) == name1);
CuAssertTrue(testCase, metaSequence_getName(metaSequence2) == name2);
cactusDiskTestTeardown();
}
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 int cactusDisk_constructMetaSequencesP(const void *o1, const void *o2) {
return cactusMisc_nameCompare(metaSequence_getName((MetaSequence *) o1), metaSequence_getName((MetaSequence *) o2));
}
static int segmentCompareFn(const void *segment1, const void *segment2) {
Name name1 = segment1 == &segmentCompareFn_coordinate ? segmentCompareFn_metaSequence : metaSequence_getName(sequence_getMetaSequence(segment_getSequence((Segment *)segment1)));
Name name2 = segment2 == &segmentCompareFn_coordinate ? segmentCompareFn_metaSequence : metaSequence_getName(sequence_getMetaSequence(segment_getSequence((Segment *)segment2)));
int i = cactusMisc_nameCompare(name1, name2);
if(i == 0) {
int64_t
x =
segment1 == &segmentCompareFn_coordinate ? segmentCompareFn_coordinate
: (int64_t) segment_getStart((void *) segment1);
int64_t
y =
segment2 == &segmentCompareFn_coordinate ? segmentCompareFn_coordinate
: (int64_t) segment_getStart((void *) segment2);
assert(
segment1 == &segmentCompareFn_coordinate || segment_getStrand(
(void *) segment1));
assert(
segment2 == &segmentCompareFn_coordinate || segment_getStrand(
(void *) segment2));
return x > y ? 1 : (x < y ? -1 : 0); //i > 0 ? 1 : i < 0 ? -1 : 0; //This was because of an overflow
}
return i;
}
Name sequence_getName(Sequence *sequence) {
return metaSequence_getName(sequence->metaSequence);
}
void testMetaSequence_getName(CuTest* testCase) {
cactusMetaSequenceTestSetup();
CuAssertTrue(testCase, metaSequence_getName(metaSequence) != NULL_NAME);
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, metaSequence_getName(metaSequence)) == metaSequence);
cactusMetaSequenceTestTeardown();
}
