BAMImporterTask::BAMImporterTask(const GUrl& url, bool _useGui, const QVariantMap &hints) :
DocumentProviderTask(tr("BAM/SAM file import: %1").arg(url.fileName()), TaskFlags_NR_FOSCOE),
loadInfoTask(NULL),
loadBamInfoTask(NULL),
prepareToImportTask(NULL),
convertTask(NULL),
loadDocTask(NULL),
isSqliteDbTransit(false),
useGui(_useGui),
sam(hints.value(SAM_HINT, false).toBool()),
hints(hints),
hintedDbiRef(hints.value(DocumentFormat::DBI_REF_HINT).value<U2DbiRef>())
{
documentDescription = url.fileName();
loadInfoTask = new LoadInfoTask( url, sam );
addSubTask(loadInfoTask);
}
void BAMImporterTask::initPrepareToImportTask() {
GUrl srcUrl = loadInfoTask->getSourceUrl();
isSqliteDbTransit = hintedDbiRef.isValid() && SQLITE_DBI_ID != hintedDbiRef.dbiFactoryId;
if (!isSqliteDbTransit) {
localDbiRef = U2DbiRef(SQLITE_DBI_ID, srcUrl.dirPath() + QDir::separator() + srcUrl.fileName() + ".ugenedb");
} else {
const QString tmpDir = AppContext::getAppSettings()->getUserAppsSettings()->getCurrentProcessTemporaryDirPath("assembly_conversion") + QDir::separator();
QDir().mkpath(tmpDir);
const QString pattern = tmpDir + "XXXXXX.ugenedb";
QTemporaryFile *tempLocalDb = new QTemporaryFile(pattern, this);
tempLocalDb->open();
const QString filePath = tempLocalDb->fileName();
tempLocalDb->close();
SAFE_POINT_EXT(QFile::exists(filePath), setError(tr("Can't create a temporary database")), );
localDbiRef = U2DbiRef(SQLITE_DBI_ID, filePath);
}
QString refUrl;
bool convert = true;
if (useGui) {
QObjectScopedPointer<ConvertToSQLiteDialog> convertDialog = new ConvertToSQLiteDialog(loadInfoTask->getSourceUrl(), loadInfoTask->getInfo(), loadInfoTask->isSam());
convertDialog->hideAddToProjectOption();
const int rc = convertDialog->exec();
CHECK_EXT(!convertDialog.isNull(), setError("NULL dialog"), );
if (rc == QDialog::Accepted) {
localDbiRef = U2DbiRef(SQLITE_DBI_ID, convertDialog->getDestinationUrl().getURLString());
refUrl = convertDialog->getReferenceUrl();
} else {
convert = false;
stateInfo.setCanceled(true);
}
} else if (loadInfoTask->isSam() && loadInfoTask->getInfo().getHeader().getReferences().isEmpty()) {