qint64 AssemblyModel::getModelHeight(U2OpStatus & os) {
if(NO_VAL == cachedModelHeight) {
U2AttributeDbi * attributeDbi = dbiHandle.dbi->getAttributeDbi();
if(attributeDbi != NULL) {
U2IntegerAttribute attr = U2AttributeUtils::findIntegerAttribute(attributeDbi, assembly.id, U2BaseAttributeName::max_prow, os);
LOG_OP(os);
if(attr.hasValidId()) {
if(attr.version == assembly.version) {
cachedModelHeight = attr.value;
} else if(checkPermissions(QFile::WriteUser,false)) {
U2AttributeUtils::removeAttribute(attributeDbi, attr.id, os);
LOG_OP(os);
}
}
}
if(cachedModelHeight == NO_VAL) {
// if could not get value from attribute, recompute the value...
cachedModelHeight = assemblyDbi->getMaxPackedRow(assembly.id, U2Region(0, getModelLength(os)), os);
LOG_OP(os);
if(! os.isCoR()) {
// ...and store it in a new attribure
U2IntegerAttribute attr;
U2AttributeUtils::init(attr, assembly, U2BaseAttributeName::max_prow);
attr.value = cachedModelHeight;
attributeDbi->createIntegerAttribute(attr, os);
}
}
if(cachedModelHeight == NO_VAL){
os.setError("Can't get model height, database is corrupted");
LOG_OP(os);
}
}
return cachedModelHeight;
}
//off_t lseek(int fd, off_t offset, int whence);
off_t posix_lseek(const char *path, int fd, off_t offset, int whence)
{
off_t ret;
char whenceBuf[16];
const char *whenceStr;
switch (whence )
{
case SEEK_SET:
whenceStr = "SEEK_SET";
break;
case SEEK_CUR:
whenceStr = "SEEK_CUR";
break;
case SEEK_END:
whenceStr = "SEEK_END";
break;
default:
snprintf(whenceBuf, sizeof(whenceBuf), "%d", whence);
whenceStr = whenceBuf;
}
ret = lseek(fd, offset, whence);
LOG_OP(ret == (off_t) -1, errno,
"lseek(fd=%d offset=%llu whence=%s) path='%s' ret=%lu",
fd, (uint64_t) offset, whenceStr, path, ret);
return ret;
}
qint64 ZoomableAssemblyOverview::minimalOverviewedLen() const {
U2OpStatusImpl os;
qint64 modelLen = model->getModelLength(os);
LOG_OP(os);
// 1 letter == 1 pixel. We are not going to draw more than one pixel per letter
// Allow more pixels per letter only if model is shorter than screen
return qMin(modelLen, (qint64)width());
}
//int dup(int fildes);
int posix_dup(const char *path, int fd)
{
int ret;
LOOP_ON_EINTR(ret = dup(fd), ret < 0, errno);;
LOG_OP(ret < 0, errno,
"dup(fd=%d) path='%s'",
fd, path);
return ret;
}
//int close(int fd);
int posix_close(const char *path, int fd)
{
int ret;
LOOP_ON_EINTR(ret = close(fd), ret < 0, errno);
LOG_OP(ret < 0, errno,
"close(fd=%d) path='%s' ret=%d",
fd, path, ret);
return ret;
}
//int open(char *path, int oflag, mode_t mode); We always use the 3 arguments version
int posix_open(const char *path, int oflag, mode_t mode)
{
int ret;
LOOP_ON_EINTR(ret = open(path, oflag, mode), ret < 0, errno);
LOG_OP(ret < 0, errno,
"open(path='%s' oflag=%#x mode=%#x) ret=%d",
path, oflag, mode, ret);
return ret;
}
//int creat(char *path, mode_t mode);
int posix_creat(const char *path, mode_t mode)
{
int ret;
LOOP_ON_EINTR(ret = creat(path, mode), ret < 0, errno);
LOG_OP(ret < 0, errno,
"creat(path='%s' mode=%#x) ret=%d",
path, mode, ret);
return ret;
}
//DIR *opendir(char *dirname);
DIR *posix_opendir(const char *dirname)
{
DIR *dirp;
dirp = opendir(dirname);
LOG_OP(dirp == NULL, errno,
"opendir(dirname='%s') dirp=%p",
dirname, dirp);
return dirp;
}
//ssize_t write(int fildes, const void *buf, size_t nbyte);
ssize_t posix_write(const char *path,
int fd, const void *buf, size_t nbyte)
{
ssize_t ret;
LOOP_ON_EINTR(ret = write(fd, buf, nbyte), ret < 0, errno);
LOG_OP(ret < 0, errno,
"write_packet(fd=%d buf=%p nbyte=%zu) path='%s' ret=%zd",
fd, buf, nbyte, path, ret);
return ret;
}
//int closedir(DIR *dirp);
int posix_closedir(const char *path, DIR *dirp)
{
//this saves the address of the pointer without
// keeping and passing the pointer itself to LOG_OP().
ptrdiff_t ptradr = (char *) dirp - (char *) 0;
int ret;
ret = closedir(dirp);
LOG_OP(ret < 0, errno,
"closedir(dirp=0x%x) path='%s' ret=%d",
ptradr, path, ret);
return ret;
}
qint64 AssemblyModel::getModelLength(U2OpStatus & os) {
if(NO_VAL == cachedModelLength) {
// try to set length from attributes
U2AttributeDbi * attributeDbi = dbiHandle.dbi->getAttributeDbi();
if(attributeDbi != NULL) {
U2IntegerAttribute attr = U2AttributeUtils::findIntegerAttribute(attributeDbi, assembly.id, U2BaseAttributeName::reference_length, os);
LOG_OP(os);
if(attr.hasValidId()) {
cachedModelLength = attr.value;
}
// ignore incorrect attribute value and remove corrupted attribute (auto-fix incorrectly converted ugenedb)
if(cachedModelLength == 0) {
coreLog.details(QString("ignored incorrect value of attribute %1: should be > 0, got %2. Bad attribute removed!").arg(QString(U2BaseAttributeName::reference_length)).arg(cachedModelLength));
cachedModelLength = NO_VAL;
U2AttributeUtils::removeAttribute(attributeDbi, attr.id, os);
}
}
// if cannot from attributes -> set from reference or max end pos
if(cachedModelLength == NO_VAL) {
qint64 refLen = hasReference() ? refObj->getSequenceLength() : 0;
qint64 assLen = assemblyDbi->getMaxEndPos(assembly.id, os);
LOG_OP(os);
cachedModelLength = qMax(refLen, assLen);
// and save in attribute
U2IntegerAttribute attr;
U2AttributeUtils::init(attr, assembly, U2BaseAttributeName::reference_length);
attr.value = cachedModelLength;
attributeDbi->createIntegerAttribute(attr, os);
}
if(cachedModelLength == NO_VAL){
os.setError("Can't get model length, database is corrupted");
LOG_OP(os);
}
}
return cachedModelLength;
}
//int select(int nfds, fd_set *readfds, fd_set *writefds, fd_set *exceptfds, struct timeval *timeout);
int posix_select(const char *path,
int nfds,
fd_set *readfds, fd_set *writefds, fd_set *exceptfds,
struct timeval *timeout)
{
int ret;
struct timeval tv;
//select() updates timeout which is not permitted by POSIX.1-2001.
// So copy the timeout and use the copy in the call.
if (timeout != NULL) {
tv = *timeout;
}
LOOP_ON_EINTR(ret = select(nfds, readfds, writefds, exceptfds, (timeout != NULL) ? &tv : NULL), ret < 0, errno);
LOG_OP(ret < 0, errno,
"select(nfds=%d readfds=%p writefds=%p exceptfds=%p timeout=%ld.%ld) path='%s' ret=%zd",
nfds, readfds, writefds, exceptfds,
(timeout != NULL) ? timeout->tv_sec : -1,
(timeout != NULL) ? timeout->tv_usec : -1,
path, ret);
return ret;
}
const U2AssemblyCoverageStat &AssemblyModel::getCoverageStat(U2OpStatus & os) {
QMutexLocker mutexLocker(&mutex);
Q_UNUSED(mutexLocker);
if(cachedCoverageStat.isEmpty()) {
U2AttributeDbi * attributeDbi = dbiHandle.dbi->getAttributeDbi();
if(NULL != attributeDbi) {
U2ByteArrayAttribute attr = U2AttributeUtils::findByteArrayAttribute(attributeDbi, assembly.id, COVERAGE_STAT_ATTRIBUTE_NAME, os);
if(!os.isCoR()) {
if(attr.hasValidId()) {
// TODO: check version
U2AssemblyUtils::deserializeCoverageStat(attr.value, cachedCoverageStat, os);
} else {
qint64 length = getModelLength(os);
if(!os.isCoR()) {
static const qint64 MAX_COVERAGE_CACHE_SIZE = 1000*1000;
int coverageCacheSize = (int)qMin(MAX_COVERAGE_CACHE_SIZE, length);
cachedCoverageStat.resize(coverageCacheSize);
calculateCoverageStat(U2Region(0, length), cachedCoverageStat, os);
if(!os.isCoR()) {
U2ByteArrayAttribute attribute;
attribute.objectId = assembly.id;
attribute.name = COVERAGE_STAT_ATTRIBUTE_NAME;
attribute.value = U2AssemblyUtils::serializeCoverageStat(cachedCoverageStat);
attribute.version = assembly.version;
U2OpStatusImpl opStatus;
attributeDbi->createByteArrayAttribute(attribute, opStatus);
LOG_OP(opStatus);
}
}
}
}
} else {
os.setError("Attribute DBI is not supported");
}
}
return cachedCoverageStat;
}
QString AssemblyBrowser::tryAddObject(GObject * obj) {
Document * objDoc = obj->getDocument();
SAFE_POINT(NULL != objDoc, "", tr("Internal error: only object with document can be added to browser"));
if (GObjectTypes::SEQUENCE == obj->getGObjectType()) {
U2SequenceObject * seqObj = qobject_cast<U2SequenceObject*>(obj);
CHECK(NULL != seqObj, tr("Internal error: broken sequence object"));
SAFE_POINT(NULL != objDoc->getDocumentFormat(), "", tr("Internal error: empty document format"));
U2OpStatus2Log os;
qint64 seqLen = seqObj->getSequenceLength();
QStringList errs;
qint64 modelLen = model->getModelLength(os);
if (seqLen != modelLen) {
errs << tr("The lengths of the sequence and assembly are different.");
}
if (seqObj->getGObjectName() != gobject->getGObjectName()) {
errs << tr("The sequence and assembly names are different.");
}
// commented: waiting for fix
//QByteArray refMd5 = model->getReferenceMd5();
//if(!refMd5.isEmpty()) {
// //QByteArray data = QString(seqObj->getSequence()).remove("-").toUpper().toUtf8();
// QByteArray data = QString(seqObj->getSequence()).toUpper().toUtf8();
// QByteArray seqObjMd5 = QCryptographicHash::hash(data, QCryptographicHash::Md5).toHex();
// if(seqObjMd5 != refMd5) {
// errs << tr("- Reference MD5 not match with MD5 written in assembly");
// }
//}
bool setRef = !isAssemblyObjectLocked(true) && !model->isLoadingReference();
setRef &= model->checkPermissions(QFile::WriteUser, setRef);
if(!errs.isEmpty() && setRef) {
const NotificationStack *notificationStack = AppContext::getMainWindow()->getNotificationStack();
const QString message = tr("It seems that sequence \"%1\", set as reference to assembly \"%2\", does not match it.").arg(seqObj->getGObjectName()).arg(gobject->getGObjectName())
+ "\n- " + errs.join("\n- ");
notificationStack->addNotification(message, Warning_Not);
}
if(setRef) {
model->setReference(seqObj);
U2Assembly assembly = model->getAssembly();
U2DataId refId;
QString folder;
const QStringList folders = model->getDbiConnection().dbi->getObjectDbi()->getObjectFolders(assembly.id, os);
if (folders.isEmpty() || os.isCoR()) {
folder = U2ObjectDbi::ROOT_FOLDER;
} else {
folder = folders.first();
}
if (seqObj->getEntityRef().dbiRef == model->getDbiConnection().dbi->getDbiRef()) {
refId = seqObj->getEntityRef().entityId;
} else {
U2CrossDatabaseReferenceDbi * crossDbi = model->getDbiConnection().dbi->getCrossDatabaseReferenceDbi();
U2CrossDatabaseReference crossDbRef;
// Cannot simply use seqObj->getSequenceRef(), since it points to a temporary dbi
// TODO: make similar method seqObj->getPersistentSequenctRef()
crossDbRef.dataRef.dbiRef.dbiId = objDoc->getURLString();
crossDbRef.dataRef.dbiRef.dbiFactoryId = "document";
crossDbRef.dataRef.entityId = seqObj->getGObjectName().toUtf8();
crossDbRef.visualName = "cross_database_reference: " + seqObj->getGObjectName();
crossDbRef.dataRef.version = 1;
crossDbi->createCrossReference(crossDbRef, folder, os);
LOG_OP(os);
refId = crossDbRef.id;
addObjectToView(obj);
}
model->associateWithReference(refId);
}
} else if (GObjectTypes::VARIANT_TRACK == obj->getGObjectType()) {
VariantTrackObject *trackObj = qobject_cast<VariantTrackObject*>(obj);
CHECK(NULL != trackObj, tr("Internal error: broken variant track object"));
model->addTrackObject(trackObj);
addObjectToView(obj);
connect(model.data(), SIGNAL(si_trackRemoved(VariantTrackObject *)), SLOT(sl_trackRemoved(VariantTrackObject *)));
} else {
