DbiConnection Database::createEmptyDbi(const QString& url, U2OpStatus& os) {
QFileInfo fi(url);
if (fi.exists()) {
os.setError(tr("File already exists: %1").arg(url));
return DbiConnection();
}
U2DbiRef dbiRef (SQLiteDbiFactory::ID, url);
DbiConnection databaseDbi (dbiRef, true, os);
SAFE_POINT_OP(os, DbiConnection());
databaseDbi.dbi->setProperty(S3_DATABASE_KEY, U2DbiOptions::U2_DBI_VALUE_ON, os);
SAFE_POINT_OP(os, DbiConnection());
return databaseDbi;
}
QList< QList<U2SingleModStep> > SQLiteModDbi::getModSteps(const U2DataId &masterObjId, qint64 version, U2OpStatus &os) {
QList< QList<U2SingleModStep> > steps;
SQLiteTransaction t(db, os);
qint64 userStepId = -1;
SQLiteWriteQuery qGetUserStepId("SELECT id FROM UserModStep WHERE object = ?1 AND version = ?2", db, os);
SAFE_POINT_OP(os, QList< QList<U2SingleModStep> >());
qGetUserStepId.bindDataId(1, masterObjId);
qGetUserStepId.bindInt64(2, version);
if (qGetUserStepId.step()) {
userStepId = qGetUserStepId.getInt64(0);
qGetUserStepId.ensureDone();
}
else if (!os.hasError()) {
os.setError("Failed to find user step ID!");
return steps;
}
SQLiteReadQuery qMultiStepId("SELECT id FROM MultiModStep WHERE userStepId = ?1", db, os);
qMultiStepId.bindInt64(1, userStepId);
SQLiteReadQuery qSingleStep("SELECT id, object, otype, oextra, version, modType, details, multiStepId FROM SingleModStep WHERE multiStepId = ?1", db, os);
while (qMultiStepId.step()) {
qint64 multiStepId = qMultiStepId.getInt64(0);
qSingleStep.reset();
qSingleStep.bindInt64(1, multiStepId);
QList<U2SingleModStep> currentMultiStepSingleSteps;
while (qSingleStep.step()) {
U2SingleModStep step;
step.id = qSingleStep.getInt64(0);
step.objectId = qSingleStep.getDataIdExt(1);
step.version = qSingleStep.getInt64(4);
step.modType = qSingleStep.getInt64(5);
step.details = qSingleStep.getBlob(6);
SAFE_POINT_OP(os, QList< QList<U2SingleModStep> >());
currentMultiStepSingleSteps.append(step);
}
steps.append(currentMultiStepSingleSteps);
}
return steps;
}
Database* Database::loadDatabase(const QString& url, U2OpStatus& os) {
U2DbiRef dbiRef (SQLiteDbiFactory::ID, url);
DbiConnection dbHandle (dbiRef, os);
SAFE_POINT_OP(os, NULL);
// ensure that DBI is a valid Session DBI
QString val = dbHandle.dbi->getProperty(S3_DATABASE_KEY, "", os);
SAFE_POINT_OP(os, NULL);
if (val != U2DbiOptions::U2_DBI_VALUE_ON) {
os.setError(tr("Not a valid S3-database file: %1").arg(url));
return NULL;
}
return new Database(dbHandle);
}
QList<Task*> PairwiseAlignmentHirschbergTask::onSubTaskFinished(Task *subTask) {
QList<Task*> res;
if (hasError() || isCanceled()) {
return res;
}
if (subTask->hasError() || subTask->isCanceled()) {
return res;
}
if (subTask == kalignSubTask) {
if (settings->inNewWindow == true) {
TaskStateInfo localStateInfo;
Project * currentProject = AppContext::getProject();
DocumentFormat * format = AppContext::getDocumentFormatRegistry()->getFormatById(BaseDocumentFormats::CLUSTAL_ALN);
Document * alignmentDoc = NULL;
QString newFileUrl = settings->resultFileName.getURLString();
changeGivenUrlIfDocumentExists(newFileUrl, currentProject);
alignmentDoc = format->createNewLoadedDocument(IOAdapterUtils::get(BaseIOAdapters::LOCAL_FILE), GUrl(newFileUrl), localStateInfo);
CHECK_OP(localStateInfo, res);
MAlignment resultMa = kalignSubTask->resultMA;
MAlignmentObject * docObject = MAlignmentImporter::createAlignment(alignmentDoc->getDbiRef(), resultMa, localStateInfo);
CHECK_OP(localStateInfo, res);
alignmentDoc->addObject(docObject);
SaveDocFlags flags = SaveDoc_Overwrite;
flags |= SaveDoc_OpenAfter;
res << new SaveDocumentTask(alignmentDoc, flags);
} else { //in current window
U2OpStatus2Log os;
DbiConnection con(settings->msaRef.dbiRef, os);
CHECK_OP(os, res);
QList<U2MsaRow> rows = con.dbi->getMsaDbi()->getRows(settings->msaRef.entityId, os);
CHECK_OP(os, res);
U2UseCommonUserModStep userModStep(settings->msaRef, os);
Q_UNUSED(userModStep);
SAFE_POINT_OP(os, res);
for (int rowNumber = 0; rowNumber < rows.length(); ++rowNumber) {
if (rows[rowNumber].sequenceId == settings->firstSequenceRef.entityId) {
con.dbi->getMsaDbi()->updateGapModel(settings->msaRef.entityId, rows[rowNumber].rowId, kalignSubTask->resultMA.getRow(0).getGapModel(), os);
CHECK_OP(os, res);
}
if (rows[rowNumber].sequenceId == settings->secondSequenceRef.entityId) {
con.dbi->getMsaDbi()->updateGapModel(settings->msaRef.entityId, rows[rowNumber].rowId, kalignSubTask->resultMA.getRow(1).getGapModel(), os);
CHECK_OP(os, res);
}
}
}
}
return res;
}
MAlignment Kalign_Load_Align_Compare_Task::dna_to_ma(QList<GObject*> dnaSeqs) {
int seqCount = dnaSeqs.count();
U2SequenceObject *seq = qobject_cast<U2SequenceObject *>(dnaSeqs[0]);
MAlignment ma("Alignment",seq->getAlphabet());
for(int i=0; i<seqCount; i++) {
seq = qobject_cast<U2SequenceObject *>(dnaSeqs[i]);
if(seq == NULL) {
stateInfo.setError( QString("Can't cast GObject to U2SequenceObject") );
return ma;
}
QByteArray seqData = seq->getWholeSequenceData(stateInfo);
SAFE_POINT_OP(stateInfo, MAlignment());
ma.addRow(seq->getSequenceName(), seqData, stateInfo);
SAFE_POINT_OP(stateInfo, MAlignment());
}
return ma;
}
QList<U2MsaRow> MAlignmentExporter::exportRows( const U2DataId &msaId, const QList<qint64> rowIds,
U2OpStatus &os ) const
{
U2MsaDbi* msaDbi = con.dbi->getMsaDbi( );
SAFE_POINT( NULL != msaDbi, NULL_MSA_DBI_ERROR, QList<U2MsaRow>( ) );
QList<U2MsaRow> result;
foreach ( qint64 rowId, rowIds ) {
result.append( msaDbi->getRow( msaId, rowId, os) );
SAFE_POINT_OP( os, QList<U2MsaRow>( ) );
}
qint64 SQLiteModDbi::getNearestUserModStepVersion(const U2DataId &masterObjId, qint64 version, U2OpStatus &os) {
SQLiteReadQuery qVersion("SELECT MAX(version) FROM UserModStep WHERE object = ?1 AND version <= ?2", db, os);
qVersion.bindDataId(1, masterObjId);
qVersion.bindInt64(2, version);
qint64 userStepVersion = version;
if (qVersion.step()) {
userStepVersion = qVersion.getInt64(0);
}
SAFE_POINT_OP(os, userStepVersion);
return userStepVersion;
}
bool TestDbiProvider::init(const QString& dbiFileName, bool _useConnectionPool){
if(initialized){
close();
initialized = false;
}
TestRunnerSettings* trs = AppContext::getAppSettings()->getTestRunnerSettings();
QString originalFile = trs->getVar("COMMON_DATA_DIR") + "/" + dbiFileName;
QString tmpFile = QDir::temp().absoluteFilePath(QFileInfo(originalFile).fileName());
if(QFile::exists(tmpFile)) {
QFile::remove(tmpFile);
}
bool _create = false;
if (QFile::exists(originalFile)) {
SAFE_POINT(QFile::copy(originalFile, tmpFile), "db file not copied", false);
}else{
_create = true;
}
dbUrl = tmpFile;
useConnectionPool = _useConnectionPool;
U2DbiFactory *factory = AppContext::getDbiRegistry()->getDbiFactoryById(SQLITE_DBI_ID);
SAFE_POINT(factory!=NULL, "No dbi factory", false);
U2OpStatusImpl opStatus;
if(useConnectionPool){
U2DbiRef ref;
ref.dbiFactoryId = factory->getId();
ref.dbiId = dbUrl;
dbi = AppContext::getDbiRegistry()->getGlobalDbiPool()->openDbi(ref, _create, opStatus);
CHECK_OP(opStatus, false);
}else{
dbi = factory->createDbi();
SAFE_POINT(NULL != dbi, "dbi not created", false);
QHash<QString, QString> properties;
if(_create){
properties[U2DbiOptions::U2_DBI_OPTION_CREATE] = U2DbiOptions::U2_DBI_VALUE_ON;
}
properties["url"] = dbUrl;
QVariantMap persistentData;
dbi->init(properties, persistentData, opStatus);
SAFE_POINT_OP(opStatus, false);
}
U2ObjectDbi* objDbi = dbi->getObjectDbi();
SAFE_POINT(NULL != objDbi, "object dbi not loaded", false);
initialized = true;
return true;
}
QString AssemblyMessageTranslator::getTranslation( ) const {
U2OpStatusImpl os;
DbiConnection connection( assemblyRef.dbiRef, os );
SAFE_POINT_OP( os, QString( ) );
U2AssemblyDbi *dbi = connection.dbi->getAssemblyDbi( );
SAFE_POINT( NULL != dbi, "Invalid assembly DBI!", QString( ) );
const U2DataId assemblyId = assemblyRef.entityId;
const qint64 assemblyLength = dbi->getMaxEndPos( assemblyId, os ) + 1;
SAFE_POINT_OP( os, QString( ) );
const U2Region wholeAssembly( 0, assemblyLength );
const qint64 countOfReads = dbi->countReads( assemblyId, wholeAssembly, os );
SAFE_POINT_OP( os, QString( ) );
QString result = QObject::tr( ASSEMBLY_LENGTH_LABEL ) + QString::number( assemblyLength )
+ INFO_FEATURES_SEPARATOR;
result += QObject::tr( COUNT_OF_READS_LABEL ) + QString::number( countOfReads );
return result;
}
Task::ReportResult GTest_SecStructPredictTask::report()
{
if (task!=NULL && task->hasError()) {
stateInfo.setError(task->getError());
} else if (!resultsTableContextName.isEmpty()) {
QList<SharedAnnotationData> results = task->getResults();
U2OpStatusImpl os;
const U2DbiRef dbiRef = AppContext::getDbiRegistry()->getSessionTmpDbiRef(os);
SAFE_POINT_OP(os, ReportResult_Finished);
aObj = new AnnotationTableObject(resultsTableContextName, dbiRef);
aObj->addAnnotations(results);
addContext(resultsTableContextName, aObj);
contextAdded = true;
}
return ReportResult_Finished;
}
AnnotationTableObject * SendSelectionDialog::getAnnotationObject() const {
if(ca_c->isNewObject()) {
U2OpStatusImpl os;
const U2DbiRef dbiRef = AppContext::getDbiRegistry( )->getSessionTmpDbiRef( os );
SAFE_POINT_OP( os, NULL );
AnnotationTableObject *aobj = new AnnotationTableObject( "Annotations", dbiRef );
aobj->addObjectRelation(GObjectRelation(ca_c->getModel().sequenceObjectRef, ObjectRole_Sequence));
return aobj;
}
else {
bool objectPrepared = ca_c->prepareAnnotationObject();
if (!objectPrepared){
QMessageBox::warning(NULL, tr("Error"), tr("Cannot create an annotation object. Please check settings"));
return NULL;
}
return ca_c->getModel().getAnnotationObject();
}
}